main.nf

#!/usr/bin/env nextflow
/*
------------------------------------------------------------------------------------------------------------
                         nf-core/eager
------------------------------------------------------------------------------------------------------------
 EAGER Analysis Pipeline. Started 2018-06-05
 #### Homepage / Documentation
 https://github.com/nf-core/eager
 #### Authors
 For a list of authors and contributors, see: https://github.com/nf-core/eager/tree/dev#authors-alphabetical
------------------------------------------------------------------------------------------------------------
*/

log.info Headers.nf_core(workflow, params.monochrome_logs)

////////////////////////////////////////////////////
/* --               PRINT HELP                 -- */
////////////////////////////////////////////////////+
def json_schema = "$projectDir/nextflow_schema.json"
if (params.help) {
    def command = "nextflow run nf-core/eager --input '*_R{1,2}.fastq.gz' -profile docker"
    log.info NfcoreSchema.params_help(workflow, params, json_schema, command)
    exit 0
}

////////////////////////////////////////////////////
/* --         VALIDATE PARAMETERS              -- */
////////////////////////////////////////////////////+
if (params.validate_params) {
    NfcoreSchema.validateParameters(params, json_schema, log)
}

// Validate BAM input isn't set to paired_end
if ( params.bam && !params.single_end ) {
  exit 1, "[nf-core/eager] error: bams can only be specified with --single_end. Please check input command."
}

// Validate that skip_collapse is only set to True for paired_end reads!
if (!has_extension(params.input, "tsv") && params.skip_collapse  && params.single_end){
    exit 1, "[nf-core/eager] error: --skip_collapse can only be set for paired_end samples."
}

// Validate not trying to both skip collapse and skip trim
if ( params.skip_collapse && params.skip_trim ) {
  exit 1, "[nf-core/eager error]: you have specified to skip both merging and trimming of paired end samples. Use --skip_adapterremoval instead."
}

// Bedtools validation
if(params.run_bedtools_coverage && !params.anno_file ){
  exit 1, "[nf-core/eager] error: you have turned on bedtools coverage, but not specified a BED or GFF file with --anno_file. Please validate your parameters."
}

// BAM filtering validation
if (!params.run_bam_filtering && params.bam_mapping_quality_threshold != 0) {
  exit 1, "[nf-core/eager] error: please turn on BAM filtering if you want to perform mapping quality filtering! Provide: --run_bam_filtering."
}

if (params.dedupper == 'dedup' && !params.mergedonly) {
    log.warn "[nf-core/eager] Warning: you are using DeDup but without specifying --mergedonly for AdapterRemoval, dedup will likely fail! See documentation for more information."
}

// Genotyping validation
if (params.run_genotyping){

  if (params.genotyping_tool == 'pileupcaller' && ( !params.pileupcaller_bedfile || !params.pileupcaller_snpfile ) ) {
    exit 1, "[nf-core/eager] error: please check your pileupCaller bed file and snp file parameters. You must supply a bed file and a snp file."
  }

  if (params.genotyping_tool == 'angsd' && ! ( params.angsd_glformat == 'text' || params.angsd_glformat == 'binary' || params.angsd_glformat == 'binary_three' || params.angsd_glformat == 'beagle' ) ) {
    exit 1, "[nf-core/eager] error: please check your ANGSD output format! Options: 'text', 'binary', 'binary_three', 'beagle'. Found parameter: --angsd_glformat '${params.angsd_glformat}'."
  }
}

// Consensus sequence generation validation
if (params.run_vcf2genome) {
    if (!params.run_genotyping) {
      exit 1, "[nf-core/eager] error: consensus sequence generation requires genotyping via UnifiedGenotyper on be turned on with the parameter --run_genotyping and --genotyping_tool 'ug'. Please check your genotyping parameters."
    }

    if (params.genotyping_tool != 'ug') {
      exit 1, "[nf-core/eager] error: consensus sequence generation requires genotyping via UnifiedGenotyper on be turned on with the parameter --run_genotyping and --genotyping_tool 'ug'. Found parameter: --genotyping_tool '${params.genotyping_tool}'."
    }
}

// MultiVCFAnalyzer validation
if (params.run_multivcfanalyzer) {
  if (!params.run_genotyping) {
    exit 1, "[nf-core/eager] error: MultiVCFAnalyzer requires genotyping to be turned on with the parameter --run_genotyping. Please check your genotyping parameters."
  }

  if (params.genotyping_tool != "ug") {
    exit 1, "[nf-core/eager] error: MultiVCFAnalyzer only accepts VCF files from GATK UnifiedGenotyper. Found parameter: --genotyping_tool '${params.genotyping_tool}'."
  }

  if (params.gatk_ploidy != 2) {
    exit 1, "[nf-core/eager] error: MultiVCFAnalyzer only accepts VCF files generated with a GATK ploidy set to 2. Found parameter: --gatk_ploidy ${params.gatk_ploidy}."
  }

  if (params.additional_vcf_files) {
      ch_extravcfs_for_multivcfanalyzer = Channel.fromPath(params.additional_vcf_files, checkIfExists: true)
  }
}

if (params.run_metagenomic_screening) {
  if ( params.bam_unmapped_type == "discard" ) {
  exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --bam_unmapped_type 'fastq'. Supplied: --bam_unmapped_type '${params.bam_unmapped_type}'."
  }

  if (params.bam_unmapped_type != 'fastq' ) {
  exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads in FASTQ format. Please supply --bam_unmapped_type 'fastq'. Found parameter: --bam_unmapped_type '${params.bam_unmapped_type}'."
  }

  if (!params.database) {
    exit 1, "[nf-core/eager] error: metagenomic classification requires a path to a database directory. Please specify one with --database '/path/to/database/'."
  }

  if (params.metagenomic_tool == 'malt' && params.malt_min_support_mode == 'percent' && params.metagenomic_min_support_reads != 1) {
    exit 1, "[nf-core/eager] error: incompatible MALT min support configuration. Percent can only be used with --malt_min_support_percent. You modified: --metagenomic_min_support_reads."
  }

  if (params.metagenomic_tool == 'malt' && params.malt_min_support_mode == 'reads' && params.malt_min_support_percent != 0.01) {
    exit 1, "[nf-core/eager] error: incompatible MALT min support configuration. Reads can only be used with --malt_min_supportreads. You modified: --malt_min_support_percent."
  }

  if (!params.metagenomic_min_support_reads.toString().isInteger()){
    exit 1, "[nf-core/eager] error: incompatible min_support_reads configuration. min_support_reads can only be used with integers. --metagenomic_min_support_reads Found parameter: ${params.metagenomic_min_support_reads}."
  }
}

// MaltExtract validation
if (params.run_maltextract) {

  if (params.run_metagenomic_screening && params.metagenomic_tool != 'malt') {
    exit 1, "[nf-core/eager] error: MaltExtract can only accept MALT output. Please supply --metagenomic_tool 'malt'. Found parameter: --metagenomic_tool '${params.metagenomic_tool}'"
  }

  if (params.run_metagenomic_screening && params.metagenomic_tool != 'malt') {
    exit 1, "[nf-core/eager] error: MaltExtract can only accept MALT output. Please supply --metagenomic_tool 'malt'. Found parameter: --metagenomic_tool '${params.metagenomic_tool}'"
  }

  if (!params.maltextract_taxon_list) {
    exit 1, "[nf-core/eager] error: MaltExtract requires a taxon list specifying the target taxa of interest. Specify the file with --params.maltextract_taxon_list."
  }
}

/////////////////////////////////////////////////////////
/* --          VALIDATE INPUT FILES                 -- */
/////////////////////////////////////////////////////////

// Set up channels for annotation file
if (!params.run_bedtools_coverage){
  ch_anno_for_bedtools = Channel.empty()
} else {
  ch_anno_for_bedtools = Channel.fromPath(params.anno_file, checkIfExists: true)
    .ifEmpty { exit 1, "[nf-core/eager] error: bedtools annotation file not found. Supplied parameter: --anno_file ${params.anno_file}."}
}

if (params.fasta) {
    file(params.fasta, checkIfExists: true)
    lastPath = params.fasta.lastIndexOf(File.separator)
    lastExt = params.fasta.lastIndexOf(".")
    fasta_base = params.fasta.substring(lastPath+1)
    index_base = params.fasta.substring(lastPath+1,lastExt)
    if (params.fasta.endsWith('.gz')) {
        fasta_base = params.fasta.substring(lastPath+1,lastExt)
        index_base = fasta_base.substring(0,fasta_base.lastIndexOf("."))

    }
} else {
    exit 1, "[nf-core/eager] error: please specify --fasta with the path to your reference"
}

// Validate reference inputs
if("${params.fasta}".endsWith(".gz")){
    process unzip_reference{
        tag "${zipped_fasta}"

        input:
        path zipped_fasta from file(params.fasta) // path doesn't like it if a string of an object is not prefaced with a root dir (/), so use file() to resolve string before parsing to `path` 

        output:
        path "$unzip" into ch_fasta into ch_fasta_for_bwaindex,ch_fasta_for_bt2index,ch_fasta_for_faidx,ch_fasta_for_seqdict,ch_fasta_for_circulargenerator,ch_fasta_for_circularmapper,ch_fasta_for_damageprofiler,ch_fasta_for_qualimap,ch_fasta_for_pmdtools,ch_fasta_for_genotyping_ug,ch_fasta_for_genotyping_hc,ch_fasta_for_genotyping_freebayes,ch_fasta_for_genotyping_pileupcaller,ch_fasta_for_vcf2genome,ch_fasta_for_multivcfanalyzer,ch_fasta_for_genotyping_angsd,ch_fasta_for_damagerescaling

        script:
        unzip = zipped_fasta.toString() - '.gz'
        """
        pigz -f -d -p ${task.cpus} $zipped_fasta
        """
        }
    } else {
    fasta_for_indexing = Channel
    .fromPath("${params.fasta}", checkIfExists: true)
    .into{ ch_fasta_for_bwaindex; ch_fasta_for_bt2index; ch_fasta_for_faidx; ch_fasta_for_seqdict; ch_fasta_for_circulargenerator; ch_fasta_for_circularmapper; ch_fasta_for_damageprofiler; ch_fasta_for_qualimap; ch_fasta_for_pmdtools; ch_fasta_for_genotyping_ug; ch_fasta__for_genotyping_hc; ch_fasta_for_genotyping_hc; ch_fasta_for_genotyping_freebayes; ch_fasta_for_genotyping_pileupcaller; ch_fasta_for_vcf2genome; ch_fasta_for_multivcfanalyzer;ch_fasta_for_genotyping_angsd;ch_fasta_for_damagerescaling }
}

// Check that fasta index file path ends in '.fai'
if (params.fasta_index && !params.fasta_index.endsWith(".fai")) {
    exit 1, "The specified fasta index file (${params.fasta_index}) is not valid. Fasta index files should end in '.fai'."
}

// Check if genome exists in the config file. params.genomes is from igenomes.conf, params.genome specified by user
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
    exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(', ')}"
}

// Index files provided? Then check whether they are correct and complete
if( params.bwa_index && (params.mapper == 'bwaaln' | params.mapper == 'bwamem' | params.mapper == 'circularmapper')){
    Channel
        .fromPath(params.bwa_index, checkIfExists: true)
        .ifEmpty { exit 1, "[nf-core/eager] error: bwa indices not found in: ${index_base}." }
        .into {bwa_index; bwa_index_bwamem}

    bt2_index = Channel.empty()
}

if( params.bt2_index && params.mapper == 'bowtie2' ){
    lastPath = params.bt2_index.lastIndexOf(File.separator)
    bt2_dir =  params.bt2_index.substring(0,lastPath+1)
    bt2_base = params.bt2_index.substring(lastPath+1)

    Channel
        .fromPath(params.bt2_index, checkIfExists: true)
        .ifEmpty { exit 1, "[nf-core/eager] error: bowtie2 indices not found in: ${bt2_dir}." }
        .into {bt2_index; bt2_index_bwamem}

    bwa_index = Channel.empty()
    bwa_index_bwamem = Channel.empty()
}

// Adapter removal adapter-list setup
if ( !params.clip_adapters_list ) {
    Channel
      .fromPath("$projectDir/assets/nf-core_eager_dummy2.txt", checkIfExists: true)
      .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
      .into {ch_adapterlist}
} else {
    Channel
      .fromPath("${params.clip_adapters_list}", checkIfExists: true)
      .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
      .into {ch_adapterlist}
}


// SexDetermination channel set up and bedfile validation
if (!params.sexdeterrmine_bedfile) {
  ch_bed_for_sexdeterrmine = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
} else {
  ch_bed_for_sexdeterrmine = Channel.fromPath(params.sexdeterrmine_bedfile, checkIfExists: true)
}

 // pileupCaller channel generation and input checks for 'random sampling' genotyping
if (!params.pileupcaller_bedfile) {
  ch_bed_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
} else {
  ch_bed_for_pileupcaller = Channel.fromPath(params.pileupcaller_bedfile, checkIfExists: true)
}

if (!params.pileupcaller_snpfile) {
  ch_snp_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt")
} else {
  ch_snp_for_pileupcaller = Channel.fromPath(params.pileupcaller_snpfile, checkIfExists: true)
}

// Create input channel for MALT database directory, checking directory exists
if ( !params.database ) {
    ch_db_for_malt = Channel.empty()
} else {
    ch_db_for_malt = Channel.fromPath(params.database, checkIfExists: true)
}

// Create input channel for MaltExtract taxon list, to allow downloading of taxon list, checking file exists.
if ( !params.maltextract_taxon_list ) {
    ch_taxonlist_for_maltextract = Channel.empty()
} else {
    ch_taxonlist_for_maltextract = Channel.fromPath(params.maltextract_taxon_list, checkIfExists: true)
}

// Create input channel for MaltExtract NCBI files, checking files exists.
if ( !params.maltextract_ncbifiles ) {
    ch_ncbifiles_for_maltextract = Channel.empty()
} else {
    ch_ncbifiles_for_maltextract = Channel.fromPath(params.maltextract_ncbifiles, checkIfExists: true)
}

////////////////////////////////////////////////////
/* --     Collect configuration parameters     -- */
////////////////////////////////////////////////////

// Check if genome exists in the config file
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
    exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(', ')}"
}

// Check AWS batch settings
if (workflow.profile.contains('awsbatch')) {
    // AWSBatch sanity checking
    if (!params.awsqueue || !params.awsregion) exit 1, 'Specify correct --awsqueue and --awsregion parameters on AWSBatch!'
    // Check outdir paths to be S3 buckets if running on AWSBatch
    // related: https://github.com/nextflow-io/nextflow/issues/813
    if (!params.outdir.startsWith('s3:')) exit 1, 'Outdir not on S3 - specify S3 Bucket to run on AWSBatch!'
    // Prevent trace files to be stored on S3 since S3 does not support rolling files.
    if (params.tracedir.startsWith('s3:')) exit 1, 'Specify a local tracedir or run without trace! S3 cannot be used for tracefiles.'
}

ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
ch_eager_logo = file("$projectDir/docs/images/nf-core_eager_logo_outline_drop.png")
ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
where_are_my_files = file("$projectDir/assets/where_are_my_files.txt")

///////////////////////////////////////////////////
/* --    INPUT FILE LOADING AND VALIDATING    -- */
///////////////////////////////////////////////////

// check if we have valid --reads or --input
if (!params.input) {
  exit 1, "[nf-core/eager] error: --input was not supplied! Please check '--help' or documentation under 'running the pipeline' for details"
}

// Read in files properly from TSV file
tsv_path = null
if (params.input && (has_extension(params.input, "tsv"))) tsv_path = params.input

ch_input_sample = Channel.empty()

if (tsv_path) {

    tsv_file = file(tsv_path)
    
    if (tsv_file instanceof List) exit 1, "[nf-core/eager] error: can only accept one TSV file per run."
    if (!tsv_file.exists()) exit 1, "[nf-core/eager] error: input TSV file could not be found. Does the file exist and is it in the right place? You gave the path: ${params.input}"

    ch_input_sample = extract_data(tsv_path)

} else if (params.input && !has_extension(params.input, "tsv")) {

    log.info ""
    log.info "No TSV file provided - creating TSV from supplied directory."
    log.info "Reading path(s): ${params.input}\n"
    inputSample = retrieve_input_paths(params.input, params.colour_chemistry, params.single_end, params.single_stranded, params.udg_type, params.bam)
    ch_input_sample = inputSample

} else exit 1, "[nf-core/eager] error: --input file(s) not correctly not supplied or improperly defined, see '--help' flag and documentation under 'running the pipeline' for details."

ch_input_sample
  .into { ch_input_sample_downstream; ch_input_sample_check }

///////////////////////////////////////////////////
/* --         INPUT CHANNEL CREATION          -- */
///////////////////////////////////////////////////

// Check we don't have any duplicate file names
ch_input_sample_check
    .map {
      it ->
        def r1 = file(it[8]).getName()
        def r2 = file(it[9]).getName()
        def bam = file(it[10]).getName()

      [r1, r2, bam]

    }
    .collect()
    .map{
      file -> 
      filenames = file
      filenames -= 'NA'
      
      if( filenames.size() != filenames.unique().size() )
          exit 1, "[nf-core/eager] error: You have duplicate input FASTQ and/or BAM file names! All files must have unique names, different directories are not sufficent. Please check your input."
    }

// Drop samples with R1/R2 to fastQ channel, BAM samples to other channel
ch_branched_input = ch_input_sample_downstream.branch{
    fastq: it[8] != 'NA' //These are all fastqs
    bam: it[10] != 'NA' //These are all BAMs
}

//Removing BAM/BAI in case of a FASTQ input
ch_fastq_channel = ch_branched_input.fastq.map {
  samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, r1, r2, bam ->
    [samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, r1, r2]
}

//Removing R1/R2 in case of BAM input
ch_bam_channel = ch_branched_input.bam.map {
  samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, r1, r2, bam ->
    [samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, bam]
}

// Prepare starting channels, here we go
ch_input_for_convertbam = Channel.empty()

ch_bam_channel
  .into { ch_input_for_convertbam; ch_input_for_indexbam; }

// Also need to send raw files for lane merging, if we want to host removed fastq
ch_fastq_channel
  .into { ch_input_for_skipconvertbam; ch_input_for_lanemerge_hostremovalfastq }
  
////////////////////////////////////////////////////
/* --         PRINT PARAMETER SUMMARY          -- */
////////////////////////////////////////////////////

log.info NfcoreSchema.params_summary_log(workflow, params, json_schema)

// Header log info
def summary = [:]
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name']         = workflow.runName
summary['Input']            = params.input
summary['Fasta Ref']        = params.fasta
summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Output dir']       = params.outdir
summary['Launch dir']       = workflow.launchDir
summary['Working dir']      = workflow.workDir
summary['Script dir']       = workflow.projectDir
summary['User']             = workflow.userName
if (workflow.profile.contains('awsbatch')) {
    summary['AWS Region']   = params.awsregion
    summary['AWS Queue']    = params.awsqueue
    summary['AWS CLI']      = params.awscli
}
summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description
if (params.config_profile_contact)     summary['Config Profile Contact']     = params.config_profile_contact
if (params.config_profile_url)         summary['Config Profile URL']         = params.config_profile_url
summary['Config Files'] = workflow.configFiles.join(', ')
if (params.email || params.email_on_fail) {
    summary['E-mail Address']    = params.email
    summary['E-mail on failure'] = params.email_on_fail
    summary['MultiQC maxsize']   = params.max_multiqc_email_size
}

Channel.from(summary.collect{ [it.key, it.value] })
    .map { k,v -> "<dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }
    .reduce { a, b -> return [a, b].join("\n            ") }
    .map { x -> """
    id: 'nf-core-eager-summary'
    description: " - this information is collected when the pipeline is started."
    section_name: 'nf-core/eager Workflow Summary'
    section_href: 'https://github.com/nf-core/eager'
    plot_type: 'html'
    data: |
        <dl class=\"dl-horizontal\">
            $x
        </dl>
    """.stripIndent() }
    .set { ch_workflow_summary }


// Check the hostnames against configured profiles
checkHostname()

log.info "Schaffa, Schaffa, Genome Baua!"

///////////////////////////////////////////////////
/* --          REFERENCE FASTA INDEXING       -- */
///////////////////////////////////////////////////

// BWA Index
if( !params.bwa_index && params.fasta && (params.mapper == 'bwaaln' || params.mapper == 'bwamem' || params.mapper == 'circularmapper')){
  process makeBWAIndex {
    label 'sc_medium'
    tag "${fasta}"
    publishDir path: "${params.outdir}/reference_genome/bwa_index", mode: params.publish_dir_mode, saveAs: { filename -> 
            if (params.save_reference) filename 
            else if(!params.save_reference && filename == "where_are_my_files.txt") filename
            else null
    }

    input:
    path fasta from ch_fasta_for_bwaindex
    path where_are_my_files

    output:
    path "BWAIndex" into (bwa_index, bwa_index_bwamem)
    path "where_are_my_files.txt"

    script:
    """
    bwa index $fasta
    mkdir BWAIndex && mv ${fasta}* BWAIndex
    """
    }
    
    bt2_index = Channel.empty()
}

// bowtie2 Index
if( !params.bt2_index && params.fasta && params.mapper == "bowtie2"){
  process makeBT2Index {
    label 'sc_medium'
    tag "${fasta}"
    publishDir path: "${params.outdir}/reference_genome/bt2_index", mode: params.publish_dir_mode, saveAs: { filename -> 
            if (params.save_reference) filename 
            else if(!params.save_reference && filename == "where_are_my_files.txt") filename
            else null
    }

    input:
    path fasta from ch_fasta_for_bt2index
    path where_are_my_files

    output:
    path "BT2Index" into (bt2_index)
    path "where_are_my_files.txt"

    script:
    """
    bowtie2-build $fasta $fasta
    mkdir BT2Index && mv ${fasta}* BT2Index
    """
    }

  bwa_index = Channel.empty()
  bwa_index_bwamem = Channel.empty()

}

// FASTA Index (FAI)
if (params.fasta_index) {
  Channel
    .fromPath( params.fasta_index )
    .set { ch_fai_for_skipfastaindexing }
} else {
  Channel
    .empty()
    .set { ch_fai_for_skipfastaindexing }
}

process makeFastaIndex {
    label 'sc_small'
    tag "${fasta}"
    publishDir path: "${params.outdir}/reference_genome/fasta_index", mode: params.publish_dir_mode, saveAs: { filename -> 
            if (params.save_reference) filename 
            else if(!params.save_reference && filename == "where_are_my_files.txt") filename
            else null
    }
    
    when: !params.fasta_index && params.fasta && ( params.mapper == 'bwaaln' || params.mapper == 'bwamem' || params.mapper == 'circularmapper')

    input:
    path fasta from ch_fasta_for_faidx
    path where_are_my_files

    output:
    path "*.fai" into ch_fasta_faidx_index
    path "where_are_my_files.txt"

    script:
    """
    samtools faidx $fasta
    """
}

ch_fai_for_skipfastaindexing.mix(ch_fasta_faidx_index) 
  .into { ch_fai_for_ug; ch_fai_for_hc; ch_fai_for_freebayes; ch_fai_for_pileupcaller; ch_fai_for_angsd }

// Stage dict index file if supplied, else load it into the channel

if (params.seq_dict) {
  Channel
    .fromPath( params.seq_dict )
    .set { ch_dict_for_skipdict }
} else {
  Channel
    .empty()
    .set { ch_dict_for_skipdict }
}

process makeSeqDict {
    label 'sc_medium'
    tag "${fasta}"
    publishDir path: "${params.outdir}/reference_genome/seq_dict", mode: params.publish_dir_mode, saveAs: { filename -> 
            if (params.save_reference) filename 
            else if(!params.save_reference && filename == "where_are_my_files.txt") filename
            else null
    }
    
    when: !params.seq_dict && params.fasta

    input:
    path fasta from ch_fasta_for_seqdict
    path where_are_my_files

    output:
    path "*.dict" into ch_seq_dict
    path "where_are_my_files.txt"

    script:
    """
    picard -Xmx${task.memory.toMega()}M CreateSequenceDictionary R=$fasta O="${fasta.baseName}.dict"
    """
}

ch_dict_for_skipdict.mix(ch_seq_dict)
  .into { ch_dict_for_ug; ch_dict_for_hc; ch_dict_for_freebayes; ch_dict_for_pileupcaller; ch_dict_for_angsd }

//////////////////////////////////////////////////
/* --         BAM INPUT PREPROCESSING        -- */
//////////////////////////////////////////////////

// Convert to FASTQ if re-mapping is requested
process convertBam {
    label 'mc_small'
    tag "$libraryid"
    
    when: 
    params.run_convertinputbam

    input: 
    tuple samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, path(bam) from ch_input_for_convertbam 

    output:
    tuple samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, path("*fastq.gz"), val('NA') into ch_output_from_convertbam

    script:
    base = "${bam.baseName}"
    """
    samtools fastq -tn ${bam} | pigz -p ${task.cpus} > ${base}.converted.fastq.gz
    """ 
}

// If not converted to FASTQ generate pipeline compatible BAM index file (i.e. with correct samtools version) 
process indexinputbam {
  label 'sc_small'
  tag "$libraryid"

  when: 
  bam != 'NA' && !params.run_convertinputbam

  input:
  tuple samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, path(bam) from ch_input_for_indexbam 

  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), file("*.{bai,csi}")  into ch_indexbam_for_filtering

  script:
  def size = params.large_ref ? '-c' : ''
  """
  samtools index ${bam} ${size}
  """
}

// convertbam bypass
    ch_input_for_skipconvertbam.mix(ch_output_from_convertbam)
        .into { ch_convertbam_for_fastp; ch_convertbam_for_fastqc } 

//////////////////////////////////////////////////
/* -- SEQUENCING QC AND FASTQ PREPROCESSING  -- */
//////////////////////////////////////////////////

// Raw sequencing QC - allow user evaluate if sequencing any good?

process fastqc {
    label 'mc_small'
    tag "${libraryid}_L${lane}"
    publishDir "${params.outdir}/fastqc/input_fastq", mode: params.publish_dir_mode,
        saveAs: { filename ->
                      filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"
                }


    input:
    tuple samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_convertbam_for_fastqc

    output:
    path "*_fastqc.{zip,html}" into ch_prefastqc_for_multiqc

    when: 
    !params.skip_fastqc

    script:
    if ( seqtype == 'PE' ) {
    """
    fastqc -t ${task.cpus} -q $r1 $r2
    rename 's/_fastqc\\.zip\$/_raw_fastqc.zip/' *_fastqc.zip
    rename 's/_fastqc\\.html\$/_raw_fastqc.html/' *_fastqc.html
    """
    } else {
    """
    fastqc -q $r1
    rename 's/_fastqc\\.zip\$/_raw_fastqc.zip/' *_fastqc.zip
    rename 's/_fastqc\\.html\$/_raw_fastqc.html/' *_fastqc.html
    """
    }
}

// Poly-G clipping for 2-colour chemistry sequencers, to reduce erroenous mapping of sequencing artefacts

if (params.complexity_filter_poly_g) {
  ch_input_for_fastp = ch_convertbam_for_fastp.branch{
    twocol: it[3] == '2' // Nextseq/Novaseq data with possible sequencing artefact
    fourcol: it[3] == '4'  // HiSeq/MiSeq data where polyGs would be true
  }

} else {
  ch_input_for_fastp = ch_convertbam_for_fastp.branch{
    twocol: it[3] == "dummy" // seq/Novaseq data with possible sequencing artefact
    fourcol: it[3] == '4' || it[3] == '2'  // HiSeq/MiSeq data where polyGs would be true
  }

}

process fastp {
    label 'mc_small'
    tag "${libraryid}_L${lane}"
    publishDir "${params.outdir}/FastP", mode: params.publish_dir_mode

    when: 
    params.complexity_filter_poly_g

    input:
    tuple samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_input_for_fastp.twocol

    output:
    tuple samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, path("*.pG.fq.gz") into ch_output_from_fastp
    path("*.json") into ch_fastp_for_multiqc

    script:
    if( seqtype == 'SE' ){
    """
    fastp --in1 ${r1} --out1 "${r1.baseName}.pG.fq.gz" -A -g --poly_g_min_len "${params.complexity_filter_poly_g_min}" -Q -L -w ${task.cpus} --json "${r1.baseName}"_L${lane}_fastp.json 
    """
    } else {
    """
    fastp --in1 ${r1} --in2 ${r2} --out1 "${r1.baseName}.pG.fq.gz" --out2 "${r2.baseName}.pG.fq.gz" -A -g --poly_g_min_len "${params.complexity_filter_poly_g_min}" -Q -L -w ${task.cpus} --json "${libraryid}"_L${lane}_polyg_fastp.json 
    """
    }
}

// Colour column only useful for fastp, so dropping now to reduce complexity downstream
ch_input_for_fastp.fourcol
  .map {
      def samplename = it[0]
      def libraryid  = it[1]
      def lane = it[2]
      def seqtype = it[4]
      def organism = it[5]
      def strandedness = it[6]
      def udg = it[7]
      def r1 = it[8]
      def r2 = seqtype == "PE" ? it[9] : file("$projectDir/assets/nf-core_eager_dummy.txt")
      
      [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]

    }
 .set { ch_skipfastp_for_merge }

ch_output_from_fastp
  .map{
    def samplename = it[0]
    def libraryid  = it[1]
    def lane = it[2]
    def seqtype = it[4]
    def organism = it[5]
    def strandedness = it[6]
    def udg = it[7]
    def r1 = it[8] instanceof ArrayList ? it[8].sort()[0] : it[8]
    def r2 = seqtype == "PE" ? it[8].sort()[1] : file("$projectDir/assets/nf-core_eager_dummy.txt")

    [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]

  }
  .set{ ch_fastp_for_merge }

ch_skipfastp_for_merge.mix(ch_fastp_for_merge)
  .into { ch_fastp_for_adapterremoval; ch_fastp_for_skipadapterremoval } 

// Sequencing adapter clipping and optional paired-end merging in preparation for mapping

process adapter_removal {
    label 'mc_small'
    tag "${libraryid}_L${lane}"
    publishDir "${params.outdir}/adapterremoval", mode: params.publish_dir_mode

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_fastp_for_adapterremoval
    path adapterlist from ch_adapterlist.collect().dump(tag: "Adapter list")

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("output/*{combined.fq,.se.truncated,pair1.truncated}.gz") into ch_output_from_adapterremoval_r1
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("output/*pair2.truncated.gz") optional true into ch_output_from_adapterremoval_r2
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("output/*.settings") into ch_adapterremoval_logs
    
    when: 
    !params.skip_adapterremoval

    script:
    def base = "${r1.baseName}_L${lane}"
    def adapters_to_remove = !params.clip_adapters_list ? "--adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor}" : "--adapter-list ${adapterlist}"
    //This checks whether we skip trimming and defines a variable respectively
    def preserve5p = params.preserve5p ? '--preserve5p' : '' // applies to any AR command - doesn't affect output file combination
    
    if ( seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim  && !params.mergedonly && !params.preserve5p ) {
    """
    mkdir -p output

    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}

    cat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
    
    mv *.settings output/

    ## Add R_ and L_ for unmerged reads for DeDup compatibility
    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz
    """
    //PE mode, collapse and trim, outputting all reads, preserving 5p
    } else if (seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim  && !params.mergedonly && params.preserve5p) {
    """
    mkdir -p output

    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}

    cat *.collapsed.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz

    mv *.settings output/

    ## Add R_ and L_ for unmerged reads for DeDup compatibility
    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1}  > output/${base}.pe.combined.fq.gz
    """
    // PE mode, collapse and trim but only output collapsed reads
    } else if ( seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim && params.mergedonly && !params.preserve5p ) {
    """
    mkdir -p output
    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe  --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
    
    cat *.collapsed.gz *.collapsed.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
        
    ## Add R_ and L_ for unmerged reads for DeDup compatibility
    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1}  > output/${base}.pe.combined.fq.gz

    mv *.settings output/
    """
    // PE mode, collapse and trim but only output collapsed reads, preserving 5p
    } else if ( seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim && params.mergedonly && params.preserve5p ) {
    """
    mkdir -p output
    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe  --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
    
    cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz
    
    ## Add R_ and L_ for unmerged reads for DeDup compatibility
    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g  output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1} > output/${base}.pe.combined.fq.gz

    mv *.settings output/
    """
    // PE mode, collapsing but skip trim, (output all reads). Note: seems to still generate `truncated` files for some reason, so merging for safety.
    // Will still do default AR length filtering I guess
    } else if ( seqtype == 'PE'  && !params.skip_collapse && params.skip_trim && !params.mergedonly ) {
    """
    mkdir -p output
    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --adapter1 "" --adapter2 ""
    
    cat *.collapsed.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
        
    ## Add R_ and L_ for unmerged reads for DeDup compatibility
    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1}  > output/${base}.pe.combined.fq.gz

    mv *.settings output/
    """
    // PE mode, collapsing but skip trim, and only output collapsed reads. Note: seems to still generate `truncated` files for some reason, so merging for safety.
    // Will still do default AR length filtering I guess
    } else if ( seqtype == 'PE'  && !params.skip_collapse && params.skip_trim && params.mergedonly ) {
    """
    mkdir -p output
    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p}  --adapter1 "" --adapter2 ""
    
    cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz
    
    ## Add R_ and L_ for unmerged reads for DeDup compatibility
    AdapterRemovalFixPrefix -Xmx${task.memory.toGiga()}g output/${base}.pe.combined.tmp.fq.gz | pigz -p ${task.cpus - 1}  > output/${base}.pe.combined.fq.gz

    mv *.settings output/
    """
    // PE mode, skip collapsing but trim (output all reads, as merging not possible) - activates paired-end mapping!
    } else if ( seqtype == 'PE'  && params.skip_collapse && !params.skip_trim ) {
    """
    mkdir -p output
    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
    
    mv ${base}.pe.pair*.truncated.gz *.settings output/
    """
    } else if ( seqtype != 'PE' && !params.skip_trim ) {
    //SE, collapse not possible, trim reads only
    """
    mkdir -p output
    AdapterRemoval --file1 ${r1} --basename ${base}.se --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
    mv *.settings *.se.truncated.gz output/
    """
    } else if ( seqtype != 'PE' && params.skip_trim ) {
    //SE, collapse not possible, trim reads only
    """
    mkdir -p output
    AdapterRemoval --file1 ${r1} --basename ${base}.se --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} ${preserve5p} --adapter1 "" --adapter2 ""
    mv *.settings *.se.truncated.gz output/
    """
    }
}

// When not collapsing paired-end data, re-merge the R1 and R2 files into single map. Otherwise if SE or collapsed PE, R2 now becomes NA
// Sort to make sure we get consistent R1 and R2 ordered when using `-resume`, even if not needed for FastQC
if ( params.skip_collapse ){
  ch_output_from_adapterremoval_r1
    .mix(ch_output_from_adapterremoval_r2)
    .groupTuple(by: [0,1,2,3,4,5,6])
    .map{
      it -> 
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]
        def r1 = file(it[7].sort()[0])
        def r2 = seqtype == "PE" ? file(it[7].sort()[1]) : file("$projectDir/assets/nf-core_eager_dummy.txt")

        [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]

    }
    .into { ch_output_from_adapterremoval; ch_adapterremoval_for_postfastqc }
} else {
  ch_output_from_adapterremoval_r1
    .map{
      it -> 
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]
        def r1 = file(it[7])
        def r2 = file("$projectDir/assets/nf-core_eager_dummy.txt")

        [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]
    }
    .into { ch_output_from_adapterremoval; ch_adapterremoval_for_postfastqc }
}

// AdapterRemoval bypass when not running it
if (!params.skip_adapterremoval) {
    ch_output_from_adapterremoval.mix(ch_fastp_for_skipadapterremoval)
        .filter { it =~/.*combined.fq.gz|.*truncated.gz/ }
        .dump(tag: "AR Bypass")
        .into { ch_adapterremoval_for_fastqc_after_clipping; ch_adapterremoval_for_lanemerge; } 
} else {
    ch_fastp_for_skipadapterremoval
        .into { ch_adapterremoval_for_fastqc_after_clipping; ch_adapterremoval_for_lanemerge; } 
}

// Lane merging for libraries sequenced over multiple lanes (e.g. NextSeq)
ch_branched_for_lanemerge = ch_adapterremoval_for_lanemerge
  .groupTuple(by: [0,1,3,4,5,6])
  .map {
    it ->
      def samplename = it[0]
      def libraryid  = it[1]
      def lane = it[2]
      def seqtype = it[3]
      def organism = it[4]
      def strandedness = it[5]
      def udg = it[6]
      def r1 = it[7]
      def r2 = it[8]

      [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]

  }
  .dump(tag: "LaneMerge Bypass")
  .branch {
    skip_merge: it[7].size() == 1 // Can skip merging if only single lanes
    merge_me: it[7].size() > 1
  }

ch_branched_for_lanemerge_skipme = ch_branched_for_lanemerge.skip_merge
  .map{
    it -> 
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]
        def r1 = it[7][0]
        def r2 = it[8][0]

        [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]
  }
  .dump(tag: "LaneMerge Reconfigure")


ch_branched_for_lanemerge_ready = ch_branched_for_lanemerge.merge_me
  .map{
      it -> 
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]
        def r1 = it[7]

        // find and remove duplicate dummies to prevent file collision error
        def r2 = it[8]*.toString()
        r2.removeAll{ it == "$projectDir/assets/nf-core_eager_dummy.txt" }

        [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]
  }

process lanemerge {
  label 'sc_tiny'
  tag "${libraryid}"
  publishDir "${params.outdir}/lanemerging", mode: params.publish_dir_mode

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(r1), path(r2) from ch_branched_for_lanemerge_ready

  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*_R1_lanemerged.fq.gz") into ch_lanemerge_for_mapping_r1
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*_R2_lanemerged.fq.gz") optional true into ch_lanemerge_for_mapping_r2

  script:
  if ( seqtype == 'PE' && ( params.skip_collapse || params.skip_adapterremoval ) ){
  lane = 0
  """
  cat ${r1} > "${libraryid}"_R1_lanemerged.fq.gz
  cat ${r2} > "${libraryid}"_R2_lanemerged.fq.gz
  """
  } else {
  """
  cat ${r1} > "${libraryid}"_R1_lanemerged.fq.gz
  """
  }

}

// Ensuring always valid R2 file even if doesn't exist for AWS
if ( ( params.skip_collapse || params.skip_adapterremoval ) ) {
  ch_lanemerge_for_mapping_r1
    .dump(tag: "Post LaneMerge Reconfigure")
    .mix(ch_lanemerge_for_mapping_r2)
    .groupTuple(by: [0,1,2,3,4,5,6])
    .map{
      it -> 
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]
        def r1 = file(it[7].sort()[0])
        def r2 = seqtype == "PE" ? file(it[7].sort()[1]) : file("$projectDir/assets/nf-core_eager_dummy.txt")

        [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]

    }
    .mix(ch_branched_for_lanemerge_skipme)
    .into { ch_lanemerge_for_skipmap; ch_lanemerge_for_bwa; ch_lanemerge_for_cm; ch_lanemerge_for_bwamem; ch_lanemerge_for_bt2 }
} else {
  ch_lanemerge_for_mapping_r1
    .map{
      it -> 
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]
        def r1 = file(it[7])
        def r2 = file("$projectDir/assets/nf-core_eager_dummy.txt")

        [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]
    }
    .mix(ch_branched_for_lanemerge_skipme)
    .into { ch_lanemerge_for_skipmap; ch_lanemerge_for_bwa; ch_lanemerge_for_cm; ch_lanemerge_for_bwamem; ch_lanemerge_for_bt2 }
}

// ENA upload doesn't do separate lanes, so merge raw FASTQs for mapped-reads removal 

// Per-library lane grouping done within process
process lanemerge_hostremoval_fastq {
  label 'sc_tiny'
  tag "${libraryid}"

  when: 
  params.hostremoval_input_fastq

  input:
  tuple samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_input_for_lanemerge_hostremovalfastq.groupTuple(by: [0,1,3,4,5,6,7])

  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.fq.gz") into ch_fastqlanemerge_for_hostremovalfastq

  script:
  if ( seqtype == 'PE' ){
  lane = 0
  """
  cat ${r1} > "${libraryid}"_R1_lanemerged.fq.gz
  cat ${r2} > "${libraryid}"_R2_lanemerged.fq.gz
  """
  } else {
  """
  cat ${r1} > "${libraryid}"_R1_lanemerged.fq.gz
  """
  }

}

// Post-preprocessing QC to help user check pre-processing removed all sequencing artefacts

process fastqc_after_clipping {
    label 'mc_small'
    tag "${libraryid}_L${lane}"
    publishDir "${params.outdir}/fastqc/after_clipping", mode: params.publish_dir_mode,
        saveAs: { filename ->
                      filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"
                }


    when: !params.skip_adapterremoval && !params.skip_fastqc

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_adapterremoval_for_fastqc_after_clipping

    output:
    path("*_fastqc.{zip,html}") into ch_fastqc_after_clipping

    script:
    if ( params.skip_collapse && seqtype == 'PE' ) {
    """
    fastqc -t ${task.cpus} -q ${r1} ${r2}
    """
    } else {
    """
    fastqc -t ${task.cpus} -q ${r1}
    """
    }

}

//////////////////////////////////////////////////
/* --    READ MAPPING AND POSTPROCESSING     -- */
//////////////////////////////////////////////////

// bwa aln as standard aDNA mapper

process bwa {
    label 'mc_medium'
    tag "${libraryid}"
    publishDir "${params.outdir}/mapping/bwa", mode: params.publish_dir_mode

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(r1), path(r2) from ch_lanemerge_for_bwa.dump(tag: "input_tuple")
    path index from bwa_index.collect().dump(tag: "input_index")

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.mapped.bam"), path("*.{bai,csi}") into ch_output_from_bwa   

    when: 
    params.mapper == 'bwaaln'

    script:
    def size = params.large_ref ? '-c' : ''
    def fasta = "${index}/${fasta_base}"

    //PE data without merging, PE data without any AR applied
    if ( seqtype == 'PE' && ( params.skip_collapse || params.skip_adapterremoval ) ){
    """
    bwa aln -t ${task.cpus} $fasta ${r1} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -o ${params.bwaalno} -f ${libraryid}.r1.sai
    bwa aln -t ${task.cpus} $fasta ${r2} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -o ${params.bwaalno} -f ${libraryid}.r2.sai
    bwa sampe -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $fasta ${libraryid}.r1.sai ${libraryid}.r2.sai ${r1} ${r2} | samtools sort -@ ${task.cpus - 1} -O bam - > ${libraryid}_"${seqtype}".mapped.bam
    samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
    """
    } else {
    //PE collapsed, or SE data
    """
    bwa aln -t ${task.cpus} ${fasta} ${r1} -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -o ${params.bwaalno} -f ${libraryid}.sai
    bwa samse -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $fasta ${libraryid}.sai $r1 | samtools sort -@ ${task.cpus - 1} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
    samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
    """
    }
    
}

// bwa mem for more complex or for modern data mapping

process bwamem {
    label 'mc_medium'
    tag "$libraryid"
    publishDir "${params.outdir}/mapping/bwamem", mode: params.publish_dir_mode

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_lanemerge_for_bwamem
    path index from bwa_index_bwamem.collect()

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.mapped.bam"), path("*.{bai,csi}") into ch_output_from_bwamem

    when: 
    params.mapper == 'bwamem'

    script:
    def split_cpus = Math.floor(task.cpus/2)
    def fasta = "${index}/${fasta_base}"
    def size = params.large_ref ? '-c' : ''

    if (!params.single_end && params.skip_collapse){
    """
    bwa mem -t ${split_cpus} $fasta $r1 $r2 -R "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" | samtools sort -@ ${split_cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
    samtools index ${size} -@ ${task.cpus} "${libraryid}".mapped.bam
    """
    } else {
    """
    bwa mem -t ${split_cpus} $fasta $r1 -R "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" | samtools sort -@ ${split_cpus} -O bam - > "${libraryid}"_"${seqtype}".mapped.bam
    samtools index -@ ${task.cpus} "${libraryid}"_"${seqtype}".mapped.bam ${size} 
    """
    }
    
}

// CircularMapper reference preparation and mapping for circular genomes e.g. mtDNA

process circulargenerator{
    label 'sc_medium'
    tag "$prefix"
    publishDir "${params.outdir}/reference_genome/circularmapper_index", mode: params.publish_dir_mode, saveAs: { filename -> 
            if (params.save_reference) filename 
            else if(!params.save_reference && filename == "where_are_my_files.txt") filename
            else null
    }


    input:
    file fasta from ch_fasta_for_circulargenerator

    output:
    file "${prefix}.{amb,ann,bwt,sa,pac}" into ch_circularmapper_indices
    file "*_elongated" into ch_circularmapper_elongatedfasta

    when: 
    params.mapper == 'circularmapper'

    script:
    prefix = "${fasta.baseName}_${params.circularextension}.fasta"
    """
    circulargenerator -Xmx${task.memory.toGiga()}g -e ${params.circularextension} -i $fasta -s ${params.circulartarget}
    bwa index $prefix
    """

}

process circularmapper{
    label 'mc_medium'
    tag "$libraryid"
    publishDir "${params.outdir}/mapping/circularmapper", mode: params.publish_dir_mode

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_lanemerge_for_cm
    file index from ch_circularmapper_indices.collect()
    file fasta from ch_fasta_for_circularmapper.collect()
    file elongated from ch_circularmapper_elongatedfasta.collect()

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.mapped.bam"), file("*.{bai,csi}") into ch_output_from_cm

    when: 
    params.mapper == 'circularmapper'

    script:
    def filter = params.circularfilter ? '-f true -x true' : ''
    def elongated_root = "${fasta.baseName}_${params.circularextension}.fasta"
    def size = params.large_ref ? '-c' : ''

    if (!params.single_end && params.skip_collapse ){
    """
    bwa aln -t ${task.cpus} $elongated_root $r1 -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.r1.sai
    bwa aln -t ${task.cpus} $elongated_root $r2 -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.r2.sai
    bwa sampe -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $elongated_root ${libraryid}.r1.sai ${libraryid}.r2.sai $r1 $r2 > tmp.out
    realignsamfile -Xmx${task.memory.toGiga()}g -e ${params.circularextension} -i tmp.out -r $fasta $filter 
    samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > ${libraryid}_"${seqtype}".mapped.bam
    samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size} 
    """
    } else {
    """ 
    bwa aln -t ${task.cpus} $elongated_root $r1 -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f ${libraryid}.sai
    bwa samse -r "@RG\\tID:ILLUMINA-${libraryid}\\tSM:${libraryid}\\tPL:illumina\\tPU:ILLUMINA-${libraryid}-${seqtype}" $elongated_root ${libraryid}.sai $r1 > tmp.out
    realignsamfile -Xmx${task.memory.toGiga()}g -e ${params.circularextension} -i tmp.out -r $fasta $filter 
    samtools sort -@ ${task.cpus} -O bam tmp_realigned.bam > "${libraryid}"_"${seqtype}".mapped.bam
    samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
    """
    }
    
}

process bowtie2 {
    label 'mc_medium'
    tag "${libraryid}"
    publishDir "${params.outdir}/mapping/bt2", mode: params.publish_dir_mode

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_lanemerge_for_bt2
    path index from bt2_index.collect()

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.mapped.bam"), path("*.{bai,csi}") into ch_output_from_bt2
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*_bt2.log") into ch_bt2_for_multiqc

    when: 
    params.mapper == 'bowtie2'

    script:
    def split_cpus = Math.floor(task.cpus/2)
    def size = params.large_ref ? '-c' : ''
    def fasta = "${index}/${fasta_base}"
    def trim5 = params.bt2_trim5 != 0 ? "--trim5 ${params.bt2_trim5}" : ""
    def trim3 = params.bt2_trim3 != 0 ? "--trim3 ${params.bt2_trim3}" : ""
    def bt2n = params.bt2n != 0 ? "-N ${params.bt2n}" : ""
    def bt2l = params.bt2l != 0 ? "-L ${params.bt2l}" : ""

    if ( "${params.bt2_alignmode}" == "end-to-end"  ) {
      switch ( "${params.bt2_sensitivity}" ) {
        case "no-preset":
        sensitivity = ""; break
        case "very-fast":
        sensitivity = "--very-fast"; break
        case "fast":
        sensitivity = "--fast"; break
        case "sensitive":
        sensitivity = "--sensitive"; break
        case "very-sensitive":
        sensitivity = "--very-sensitive"; break
        default:
        sensitivity = ""; break
        }
      } else if ("${params.bt2_alignmode}" == "local") {
      switch ( "${params.bt2_sensitivity}" ) {
        case "no-preset":
        sensitivity = ""; break
        case "very-fast":
        sensitivity = "--very-fast-local"; break
        case "fast":
        sensitivity = "--fast-local"; break
        case "sensitive":
        sensitivity = "--sensitive-local"; break
        case "very-sensitive":
        sensitivity = "--very-sensitive-local"; break
        default:
        sensitivity = ""; break

        }
      }

    //PE data without merging, PE data without any AR applied
    if ( seqtype == 'PE' && ( params.skip_collapse || params.skip_adapterremoval ) ){
    """
    bowtie2 -x ${fasta} -1 ${r1} -2 ${r2} -p ${split_cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} --maxins ${params.bt2_maxins} --rg-id ILLUMINA-${libraryid} --rg SM:${libraryid} --rg PL:illumina --rg PU:ILLUMINA-${libraryid}-${seqtype} 2> "${libraryid}"_bt2.log | samtools sort -@ ${split_cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
    samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
    """
    } else {
    //PE collapsed, or SE data 
    """
    bowtie2 -x ${fasta} -U ${r1} -p ${split_cpus} ${sensitivity} ${bt2n} ${bt2l} ${trim5} ${trim3} --rg-id ILLUMINA-${libraryid} --rg SM:${libraryid} --rg PL:illumina --rg PU:ILLUMINA-${libraryid}-${seqtype} 2> "${libraryid}"_bt2.log | samtools sort -@ ${split_cpus} -O bam > "${libraryid}"_"${seqtype}".mapped.bam
    samtools index "${libraryid}"_"${seqtype}".mapped.bam ${size}
    """
    }
    
}

// Gather all mapped BAMs from all possible mappers into common channels to send downstream
ch_output_from_bwa.mix(ch_output_from_bwamem, ch_output_from_cm, ch_indexbam_for_filtering, ch_output_from_bt2)
  .into { ch_mapping_for_hostremovalfastq; ch_mapping_for_seqtype_merging }

// Synchronise the mapped input FASTQ and input non-remapped BAM channels
ch_fastqlanemerge_for_hostremovalfastq
    .map {
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]
        def r1 = seqtype == "PE" ? file(it[7].sort()[0]) : file(it[7])
        def r2 = seqtype == "PE" ? file(it[7].sort()[1]) : file("$projectDir/assets/nf-core_eager_dummy.txt")

        [ samplename, libraryid, lane, seqtype, organism, strandedness, udg, r1, r2 ]

    }
    .mix(ch_mapping_for_hostremovalfastq)
    .groupTuple(by: [0,1,3,4,5,6])
    .map {
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]
        def r1 = it[7][0]
        def r2 = it[8][0]
        def bam = it[7][1]
        def bai = it[8][1]

      [ samplename, libraryid, seqtype, organism, strandedness, udg, r1, r2, bam, bai ]

    }
    .filter{ it[8] != null }
    .set { ch_synced_for_hostremovalfastq }

// Remove mapped reads from original (lane merged) input FASTQ e.g. for sensitive host data when running metagenomic data

process hostremoval_input_fastq {
    label 'mc_medium'
    tag "${libraryid}"
    publishDir "${params.outdir}/hostremoved_fastq", mode: params.publish_dir_mode

    when: 
    params.hostremoval_input_fastq

    input: 
    tuple samplename, libraryid, seqtype, organism, strandedness, udg, file(r1), file(r2), file(bam), file(bai) from ch_synced_for_hostremovalfastq

    output:
    tuple samplename, libraryid, seqtype, organism, strandedness, udg, file("*.fq.gz") into ch_output_from_hostremovalfastq

    script:
    if ( seqtype == 'SE' ) {
        out_fwd = bam.baseName+'.hostremoved.fq.gz'
        """
        samtools index $bam
        extract_map_reads.py $bam ${r1} -m ${params.hostremoval_mode} -of $out_fwd -p ${task.cpus}
        """
    } else {
        out_fwd = bam.baseName+'.hostremoved.fwd.fq.gz'
        out_rev = bam.baseName+'.hostremoved.rev.fq.gz'
        """
        samtools index $bam
        extract_map_reads.py $bam ${r1} -rev ${r2} -m  ${params.hostremoval_mode} -of $out_fwd -or $out_rev -p ${task.cpus}
        """ 
    }
    
}

// Seqtype merging to combine paired end with single end  sequenceing data of the same libraries
// goes here, goes into flagstat, filter etc. Important: This type of merge of this isn't technically valid for DeDup!
// and should only be used with markduplicates!
ch_branched_for_seqtypemerge = ch_mapping_for_seqtype_merging
  .groupTuple(by: [0,1,4,5,6])
  .map {
    it ->
      def samplename = it[0]
      def libraryid  = it[1]
      def lane = it[2]
      def seqtype = it[3].unique() // How to deal with this?
      def organism = it[4]
      def strandedness = it[5]
      def udg = it[6]
      def r1 = it[7]
      def r2 = it[8]

      // We will assume if mixing it is better to set as PE as this is informative
      // for DeDup (and markduplicates doesn't care), but will throw a warning!
      def seqtype_new = seqtype.flatten().size() > 1 ? 'PE' : seqtype 
                      
      if ( seqtype.flatten().size() > 1 &&  params.dedupper == 'dedup' ) {
        log.warn "[nf-core/eager] Warning: you are running DeDup on BAMs with a mixture of PE/SE data for library: ${libraryid}. DeDup is designed for PE data only, deduplication maybe suboptimal!"
      }
      
      [ samplename, libraryid, lane, seqtype_new, organism, strandedness, udg, r1, r2 ]

  }
  .dump(tag: "Seqtype")
  .branch {
    skip_merge: it[7].size() == 1 // Can skip merging if only single lanes
    merge_me: it[7].size() > 1
  }

  process seqtype_merge {

    label 'sc_tiny'
    tag "$libraryid"

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_branched_for_seqtypemerge.merge_me

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*_seqtypemerged_rg.bam"), file("*_seqtypemerged_rg*.{bai,csi}")  into ch_seqtypemerge_for_filtering

    script:
    def size = params.large_ref ? '-c' : ''
    """
    samtools merge ${libraryid}_seqtypemerged.bam ${bam}
    ## Have to set validation as lenient because of BWA issue: "I see a read stands out the end of a chromosome and is flagged as unmapped (flag 0x4). [...]" http://bio-bwa.sourceforge.net/
    picard -Xmx${task.memory.toGiga()}g AddOrReplaceReadGroups I=${libraryid}_seqtypemerged.bam O=${libraryid}_seqtypemerged_rg.bam RGID=1 RGLB="${libraryid}_seqtypemerged" RGPL=illumina RGPU=4410 RGSM="${libraryid}_seqtypemerged" VALIDATION_STRINGENCY=LENIENT
    samtools index ${libraryid}_seqtypemerged_rg.bam ${size}
    """
    
  }

ch_seqtypemerge_for_filtering
  .mix(ch_branched_for_seqtypemerge.skip_merge)
  .into { ch_seqtypemerged_for_skipfiltering; ch_seqtypemerged_for_samtools_filter; ch_seqtypemerged_for_samtools_flagstat } 

// Post-mapping QC

process samtools_flagstat {
    label 'sc_tiny'
    tag "$libraryid"
    publishDir "${params.outdir}/samtools/stats", mode: params.publish_dir_mode

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_seqtypemerged_for_samtools_flagstat


    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*stats") into ch_flagstat_for_multiqc,ch_flagstat_for_endorspy

    script:
    """
    samtools flagstat $bam > ${libraryid}_flagstat.stats
    """
}


// BAM filtering e.g. to extract unmapped reads for downstream or stricter mapping quality

process samtools_filter {
    label 'mc_medium'
    tag "$libraryid"
    publishDir "${params.outdir}/samtools/filter", mode: params.publish_dir_mode,
    saveAs: {filename ->
            if (filename.indexOf(".fq.gz") > 0) "$filename"
            else if (filename.indexOf(".unmapped.bam") > 0) "$filename"
            else if (filename.indexOf(".filtered.bam")) "$filename"
            else null
    }

    when: 
    params.run_bam_filtering

    input: 
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_seqtypemerged_for_samtools_filter

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*filtered.bam"), file("*.{bai,csi}") into ch_output_from_filtering
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.unmapped.fastq.gz") optional true into ch_bam_filtering_for_metagenomic,ch_metagenomic_for_skipentropyfilter
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.unmapped.bam") optional true

    script:
    
    def size = params.large_ref ? '-c' : ''
    
    // Unmapped/MAPQ Filtering WITHOUT min-length filtering
    if ( "${params.bam_unmapped_type}" == "keep"  && params.bam_filter_minreadlength == 0 ) {
        """
        samtools view -h ${bam} -@ ${task.cpus} -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
        samtools index ${libraryid}.filtered.bam ${size}
        """
    } else if ( "${params.bam_unmapped_type}" == "discard" && params.bam_filter_minreadlength == 0 ){
        """
        samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
        samtools index ${libraryid}.filtered.bam ${size}
        """
    } else if ( "${params.bam_unmapped_type}" == "bam" && params.bam_filter_minreadlength == 0 ){
        """
        samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
        samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
        samtools index ${libraryid}.filtered.bam ${size}
        """
    } else if ( "${params.bam_unmapped_type}" == "fastq" && params.bam_filter_minreadlength == 0 ){
        """
        samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
        samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
        samtools index ${libraryid}.filtered.bam ${size}

        ## FASTQ
        samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus - 1} > ${libraryid}.unmapped.fastq.gz
        rm ${libraryid}.unmapped.bam
        """
    } else if ( "${params.bam_unmapped_type}" == "both" && params.bam_filter_minreadlength == 0 ){
        """
        samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
        samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > ${libraryid}.filtered.bam
        samtools index ${libraryid}.filtered.bam ${size}
        
        ## FASTQ
        samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus -1} > ${libraryid}.unmapped.fastq.gz
        """
    // Unmapped/MAPQ Filtering WITH min-length filtering
    } else if ( "${params.bam_unmapped_type}" == "keep" && params.bam_filter_minreadlength != 0 ) {
        """
        samtools view -h ${bam} -@ ${task.cpus} -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
        filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
        samtools index ${libraryid}.filtered.bam ${size}
        """
    } else if ( "${params.bam_unmapped_type}" == "discard" && params.bam_filter_minreadlength != 0 ){
        """
        samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
        filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
        samtools index ${libraryid}.filtered.bam ${size}
        """
    } else if ( "${params.bam_unmapped_type}" == "bam" && params.bam_filter_minreadlength != 0 ){
        """
        samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
        samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
        filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
        samtools index ${libraryid}.filtered.bam ${size}
        """
    } else if ( "${params.bam_unmapped_type}" == "fastq" && params.bam_filter_minreadlength != 0 ){
        """
        samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
        samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
        filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
        samtools index ${libraryid}.filtered.bam ${size}

        ## FASTQ
        samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus - 1} > ${libraryid}.unmapped.fastq.gz
        rm ${libraryid}.unmapped.bam
        """
    } else if ( "${params.bam_unmapped_type}" == "both" && params.bam_filter_minreadlength != 0 ){
        """
        samtools view -h ${bam} -@ ${task.cpus} -f4 -b > ${libraryid}.unmapped.bam
        samtools view -h ${bam} -@ ${task.cpus} -F4 -q ${params.bam_mapping_quality_threshold} -b > tmp_mapped.bam
        filter_bam_fragment_length.py -a -l ${params.bam_filter_minreadlength} -o ${libraryid} tmp_mapped.bam
        samtools index ${libraryid}.filtered.bam ${size}
        
        ## FASTQ
        samtools fastq -tn ${libraryid}.unmapped.bam | pigz -p ${task.cpus} > ${libraryid}.unmapped.fastq.gz
        """
    }
}

// samtools_filter bypass in case not run
if (params.run_bam_filtering) {
    ch_seqtypemerged_for_skipfiltering.mix(ch_output_from_filtering)
        .filter { it =~/.*filtered.bam/ }
        .into { ch_filtering_for_skiprmdup; ch_filtering_for_dedup; ch_filtering_for_markdup; ch_filtering_for_flagstat; ch_skiprmdup_for_libeval; ch_mapped_for_preseq } 

} else {
    ch_seqtypemerged_for_skipfiltering
        .into { ch_filtering_for_skiprmdup; ch_filtering_for_dedup; ch_filtering_for_markdup; ch_filtering_for_flagstat; ch_skiprmdup_for_libeval; ch_mapped_for_preseq } 

}

// Post filtering mapping QC - particularly to help see how much was removed from mapping quality filtering

process samtools_flagstat_after_filter {
    label 'sc_tiny'
    tag "$libraryid"
    publishDir "${params.outdir}/samtools/filtered_stats", mode: params.publish_dir_mode

    when:
    params.run_bam_filtering

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_filtering_for_flagstat

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.stats") into ch_bam_filtered_flagstat_for_multiqc, ch_bam_filtered_flagstat_for_endorspy

    script:
    """
    samtools flagstat $bam > ${libraryid}_postfilterflagstat.stats
    """
}

if (params.run_bam_filtering) {
  ch_flagstat_for_endorspy
    .join(ch_bam_filtered_flagstat_for_endorspy, by: [0,1,2,3,4,5,6])
    .set{ ch_allflagstats_for_endorspy }

} else {
  // Add a file entry to match expected no. tuple elements for endorS.py even if not giving second file
  ch_flagstat_for_endorspy
    .map { it -> 
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]     
        def stats = file(it[7])
        def poststats = file("$projectDir/assets/nf-core_eager_dummy.txt")

      [samplename, libraryid, lane, seqtype, organism, strandedness, udg, stats, poststats ] }
    .set{ ch_allflagstats_for_endorspy }
}

// Endogenous DNA calculator to say how much of a library contained 'on-target' DNA

process endorSpy {
    label 'sc_tiny'
    tag "$libraryid"
    publishDir "${params.outdir}/endorspy", mode: params.publish_dir_mode

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(stats), path(poststats) from ch_allflagstats_for_endorspy

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.json") into ch_endorspy_for_multiqc

    script:
    if (params.run_bam_filtering) {
      """
      endorS.py -o json -n ${libraryid} ${stats} ${poststats}
      """
    } else {
      """
      endorS.py -o json -n ${libraryid} ${stats}
      """
    }
}

// Post-mapping PCR amplicon removal because these lab artefacts inflate coverage statistics

process dedup{
    label 'mc_small'
    tag "${libraryid}"
    publishDir "${params.outdir}/deduplication/", mode: params.publish_dir_mode,
        saveAs: {filename -> "${libraryid}/$filename"}

    when:
    !params.skip_deduplication && params.dedupper == 'dedup'

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_filtering_for_dedup

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.hist") into ch_hist_for_preseq
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.json") into ch_dedup_results_for_multiqc
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("${libraryid}_rmdup.bam"), path("*.{bai,csi}") into ch_output_from_dedup, ch_dedup_for_libeval

    script:
    def treat_merged = params.dedup_all_merged ? '-m' : ''
    def size = params.large_ref ? '-c' : ''
    
    if ( bam.baseName != libraryid ) {
    // To make sure direct BAMs have a clean name
    """
    mv ${bam} ${libraryid}.bam
    dedup -Xmx${task.memory.toGiga()}g -i ${libraryid}.bam $treat_merged -o . -u 
    mv *.log dedup.log
    samtools sort -@ ${task.cpus} "${libraryid}"_rmdup.bam -o "${libraryid}"_rmdup.bam
    samtools index "${libraryid}"_rmdup.bam ${size}
    """
    } else {
    """
    dedup -Xmx${task.memory.toGiga()}g -i ${libraryid}.bam $treat_merged -o . -u 
    mv *.log dedup.log
    samtools sort -@ ${task.cpus} "${libraryid}"_rmdup.bam -o "${libraryid}"_rmdup.bam
    samtools index "${libraryid}"_rmdup.bam ${size}
    """
    }
}

process markduplicates{
    label 'mc_small'
    tag "${libraryid}"
    publishDir "${params.outdir}/deduplication/", mode: params.publish_dir_mode,
        saveAs: {filename -> "${libraryid}/$filename"}

    when:
    !params.skip_deduplication && params.dedupper == 'markduplicates'

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_filtering_for_markdup

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.metrics") into ch_markdup_results_for_multiqc
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("${libraryid}_rmdup.bam"), path("*.{bai,csi}") into ch_output_from_markdup, ch_markdup_for_libeval

    script:
    def size = params.large_ref ? '-c' : ''

    if ( bam.baseName != libraryid ) {
    // To make sure direct BAMs have a clean name
    """
    mv ${bam} ${libraryid}.bam
    picard -Xmx${task.memory.toMega()}M MarkDuplicates INPUT=${libraryid}.bam OUTPUT=${libraryid}_rmdup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${libraryid}_rmdup.metrics" VALIDATION_STRINGENCY=SILENT
    samtools index ${libraryid}_rmdup.bam ${size}
    """
    } else {
    """
    picard -Xmx${task.memory.toMega()}M MarkDuplicates INPUT=${libraryid}.bam OUTPUT=${libraryid}_rmdup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE="${libraryid}_rmdup.metrics" VALIDATION_STRINGENCY=SILENT
    samtools index ${libraryid}_rmdup.bam ${size}
    """
    }

}

// This is for post-deduplcation per-library evaluation steps _without_ any 
// form of library merging. 
if ( params.skip_deduplication ) {
  ch_skiprmdup_for_libeval.mix(ch_dedup_for_libeval, ch_markdup_for_libeval)
    .into{ ch_rmdup_for_preseq; ch_rmdup_for_damageprofiler; ch_for_nuclear_contamination; ch_rmdup_formtnucratio }
} else {
  ch_dedup_for_libeval.mix(ch_markdup_for_libeval)
    .into{ ch_rmdup_for_preseq; ch_rmdup_for_damageprofiler; ch_for_nuclear_contamination; ch_rmdup_formtnucratio }
}

// Merge independent libraries sequenced but with same treatment (often done to 
// improve complexity) with the same _sample_ name. Different strand/UDG libs 
// not merged because bamtrim/pmdtools/genotyping needs that info.

// Step one: work out which are single libraries (from skipping rmdup and both dedups) that do not need merging and pass to a skipping
if ( params.skip_deduplication ) {
  ch_input_for_librarymerging = ch_filtering_for_skiprmdup
    .groupTuple(by:[0,4,5,6])
    .branch{
      clean_libraryid: it[7].size() == 1
      merge_me: it[7].size() > 1
    }
} else {
    ch_input_for_librarymerging = ch_output_from_dedup.mix(ch_output_from_markdup)
    .groupTuple(by:[0,4,5,6])
    .branch{
      clean_libraryid: it[7].size() == 1
      merge_me: it[7].size() > 1
    }
}

// For non-merging libraries, fix group libraryIDs into single values. 
// This is a bit hacky as theoretically could have different, but this should
// rarely be the case.
ch_input_for_librarymerging.clean_libraryid
  .map{
    it ->
      def libraryid = it[1][0]
      def bam = it[7].flatten()
      def bai = it[8].flatten()

      [it[0], libraryid, it[2], it[3], it[4], it[5], it[6], bam, bai ]
    }
  .set { ch_input_for_skiplibrarymerging }

ch_input_for_librarymerging.merge_me
  .map{
    it ->
      def libraryid = it[1][0]
      def seqtype = "merged"
      def bam = it[7].flatten()
      def bai = it[8].flatten()

      [it[0], libraryid, it[2], seqtype, it[4], it[5], it[6], bam, bai ]
    }
  .set { ch_fixedinput_for_librarymerging }

process library_merge {
  label 'sc_tiny'
  tag "${samplename}"
  publishDir "${params.outdir}/merged_bams/initial", mode: params.publish_dir_mode

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_fixedinput_for_librarymerging.dump(tag: "Input Tuple Library Merge")

  output:
  tuple samplename, val("${samplename}_libmerged"), lane, seqtype, organism, strandedness, udg, path("*_libmerged_rg_rmdup.bam"), path("*_libmerged_rg_rmdup.bam.{bai,csi}") into ch_output_from_librarymerging

  script:
  def size = params.large_ref ? '-c' : ''
  """
  samtools merge ${samplename}_libmerged_rmdup.bam ${bam}
  ## Have to set validation as lenient because of BWA issue: "I see a read stands out the end of a chromosome and is flagged as unmapped (flag 0x4). [...]" http://bio-bwa.sourceforge.net/
  picard -Xmx${task.memory.toGiga()}g AddOrReplaceReadGroups I=${samplename}_libmerged_rmdup.bam O=${samplename}_libmerged_rg_rmdup.bam RGID=1 RGLB="${samplename}_merged" RGPL=illumina RGPU=4410 RGSM="${samplename}_merged" VALIDATION_STRINGENCY=LENIENT
  samtools index ${samplename}_libmerged_rg_rmdup.bam ${size}
  """
}

// Mix back in libraries from skipping dedup, skipping library merging
if (!params.skip_deduplication) {
    ch_input_for_skiplibrarymerging.mix(ch_output_from_librarymerging)
        .filter { it =~/.*_rmdup.bam/ }
        .into { ch_rmdup_for_skipdamagemanipulation;  ch_rmdup_for_pmdtools; ch_rmdup_for_bamutils; ch_rmdup_for_bedtools; ch_rmdup_for_damagerescaling } 

} else {
    ch_input_for_skiplibrarymerging.mix(ch_output_from_librarymerging)
        .into { ch_rmdup_for_skipdamagemanipulation; ch_rmdup_for_pmdtools; ch_rmdup_for_bamutils; ch_rmdup_for_bedtools; ch_rmdup_for_damagerescaling } 
}

//////////////////////////////////////////////////
/* --     POST DEDUPLICATION EVALUATION      -- */
//////////////////////////////////////////////////

// Library complexity calculation from mapped reads - could a user cost-effectively sequence deeper for more unique information?
if ( params.skip_deduplication ) {
  ch_input_for_preseq = ch_rmdup_for_preseq.map{ it[0,1,2,3,4,5,6,7] }

} else if ( !params.skip_deduplication && params.dedupper == "markduplicates" ) {
  ch_input_for_preseq = ch_mapped_for_preseq.map{ it[0,1,2,3,4,5,6,7] }

} else if ( !params.skip_deduplication && params.dedupper == "dedup" ) {
  ch_input_for_preseq = ch_hist_for_preseq

}

process preseq {
    label 'sc_tiny'
    tag "${libraryid}"
    publishDir "${params.outdir}/preseq", mode: params.publish_dir_mode

    when:
    !params.skip_preseq

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(input) from ch_input_for_preseq

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("${input.baseName}.ccurve") into ch_preseq_for_multiqc

    script:
    pe_mode = params.skip_collapse && seqtype == "PE" ? '-P' : ''
    if(!params.skip_deduplication && params.dedupper == "dedup"){
    """
    preseq c_curve -s ${params.preseq_step_size} -o ${input.baseName}.ccurve -H ${input}
    """
    } else if( !params.skip_deduplication && params.dedupper == "markduplicates"){
    """
    preseq c_curve -s ${params.preseq_step_size} -o ${input.baseName}.ccurve -B ${input} ${pe_mode}
    """
    } else if ( params.skip_deduplication ) {
    """
    preseq c_curve -s ${params.preseq_step_size} -o ${input.baseName}.ccurve -B ${input} ${pe_mode}
    """
    }
}

// Optional mapping statistics for specific annotations - e.g. genes in bacterial genome

process bedtools {
  label 'mc_small'
  tag "${libraryid}"
  publishDir "${params.outdir}/bedtools", mode: params.publish_dir_mode

  when:
  params.run_bedtools_coverage

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_rmdup_for_bedtools
  file anno_file from ch_anno_for_bedtools.collect()

  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*")

  script:
  """
  bedtools coverage -nonamecheck -a ${anno_file} -b $bam | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
  bedtools coverage -nonamecheck -a ${anno_file} -b $bam -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
  """
}

//////////////////////////////////////////////////////////////
/* --    ANCIENT DNA EVALUATION AND BAM MODIFICATION     -- */
//////////////////////////////////////////////////////////////

// Calculate typical aDNA damage frequency distribution

process damageprofiler {
    label 'sc_small'
    tag "${libraryid}"

    publishDir "${params.outdir}/damageprofiler", mode: params.publish_dir_mode

    when:
    !params.skip_damage_calculation

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_rmdup_for_damageprofiler
    file fasta from ch_fasta_for_damageprofiler.collect()

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("${base}/*.txt") optional true
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("${base}/*.log")
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("${base}/*.pdf") optional true
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("${base}/*.json") optional true into ch_damageprofiler_results

    script:
    base = "${bam.baseName}"
    """
    damageprofiler -Xmx${task.memory.toGiga()}g -i $bam -r $fasta -l ${params.damageprofiler_length} -t ${params.damageprofiler_threshold} -o . -yaxis_damageplot ${params.damageprofiler_yaxis}
    """
}

// Damage rescaling with mapDamage

process mapdamage_rescaling {

    label 'sc_small'
    tag "${libraryid}"

    publishDir "${params.outdir}/damage_rescaling", mode: params.publish_dir_mode

    when:
    params.run_mapdamage_rescaling

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_rmdup_for_damagerescaling
    file fasta from ch_fasta_for_damagerescaling.collect()

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*_rescaled.bam"), path("*rescaled.bam.{bai,csi}") into ch_output_from_damagerescaling

    script:
    def base = "${bam.baseName}"
    def singlestranded = strandedness == "single" ? '--single-stranded' : ''
    def size = params.large_ref ? '-c' : ''
    """
    mapDamage -i ${bam} -r ${fasta} --rescale --rescale-out ${base}_rescaled.bam --rescale-length-5p ${params.rescale_length_5p} --rescale-length-3p=${params.rescale_length_3p} ${singlestranded}
    samtools index ${base}_rescaled.bam ${size}
    """

}

// Optionally perform further aDNA evaluation or filtering for just reads with damage etc.

process pmdtools {
    label 'mc_medium'
    tag "${libraryid}"
    publishDir "${params.outdir}/pmdtools", mode: params.publish_dir_mode

    when: params.run_pmdtools

    input: 
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_rmdup_for_pmdtools
    file fasta from ch_fasta_for_pmdtools.collect()

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.pmd.bam"), path("*.pmd.bam.{bai,csi}") into ch_output_from_pmdtools
    file "*.cpg.range*.txt"

    script:
    //Check which treatment for the libraries was used
    def treatment = udg ? (udg == 'half' ? '--UDGhalf' : '--CpG') : '--UDGminus'
    if(params.snpcapture_bed){
        snpcap = (params.pmdtools_reference_mask) ? "--refseq ${params.pmdtools_reference_mask}" : ''
        log.info"######No reference mask specified for PMDtools, therefore ignoring that for downstream analysis!"
    } else {
        snpcap = ''
    }
    def size = params.large_ref ? '-c' : ''
    def platypus = params.pmdtools_platypus ? '--platypus' : ''
    """
    #Run Filtering step 
    samtools calmd ${bam} ${fasta} | pmdtools --threshold ${params.pmdtools_threshold} ${treatment} ${snpcap} --header | samtools view -Sb - > "${libraryid}".pmd.bam
    
    #Run Calc Range step
    ## To allow early shut off of pipe: https://github.com/nextflow-io/nextflow/issues/1564
    trap 'if [[ \$? == 141 ]]; then echo "Shutting samtools early due to -n parameter" && samtools index ${libraryid}.pmd.bam ${size}; exit 0; fi' EXIT
    samtools calmd ${bam} ${fasta} | pmdtools --deamination ${platypus} --range ${params.pmdtools_range} ${treatment} ${snpcap} -n ${params.pmdtools_max_reads} > "${libraryid}".cpg.range."${params.pmdtools_range}".txt
    
    samtools index ${libraryid}.pmd.bam ${size}
    """
}

// BAM Trimming for just non-UDG or half-UDG libraries to remove damage prior genotyping

if ( params.run_trim_bam ) {

    // You wouldn't want to make UDG treated reads even shorter, so skip trimming if UDG.
    // We assume same trim amount for both non-UDG/UDG half as could trim a bit more off half-UDG to match non-UDG if needed, with minimal effect 
    // Note: Trimming of e.g. adapters are sequencing artefacts and should be removed before mapping, so we don't account for this here.
    ch_bamutils_decision = ch_rmdup_for_bamutils.branch{
        totrim: it[6] == 'none' || it[6] == 'half' 
        notrim: it[6] == 'full'
    }

} else {

    ch_bamutils_decision = ch_rmdup_for_bamutils.branch{
        totrim: it[6] == "dummy"
        notrim: it[6] == 'full' || it[6] == 'none' || it[6] == 'half'
    }

}

process bam_trim {
    label 'mc_small'
    tag "${libraryid}" 
    publishDir "${params.outdir}/trimmed_bam", mode: params.publish_dir_mode

    when: params.run_trim_bam

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_bamutils_decision.totrim

    output: 
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.trimmed.bam"), file("*.trimmed.bam.{bai,csi}") into ch_trimmed_from_bamutils

    script:
    def softclip = params.bamutils_softclip ? '-c' : '' 
    def size = params.large_ref ? '-c' : ''
    def left_clipping = udg == "half" ? "${params.bamutils_clip_half_udg_left}" : "${params.bamutils_clip_none_udg_left}"
    def right_clipping = udg == "half" ? "${params.bamutils_clip_half_udg_right}" : "${params.bamutils_clip_none_udg_right}"
    """
    bam trimBam $bam tmp.bam -L ${left_clipping} -R ${right_clipping} ${softclip}
    samtools sort -@ ${task.cpus} tmp.bam -o ${libraryid}.trimmed.bam 
    samtools index ${libraryid}.trimmed.bam ${size}
    """
}

// Post-trimming merging of libraries to single samples, except for SS/DS 
// libraries as they should be genotyped separately, because we will assume 
// that if trimming is turned on, 'lab-removed' libraries can be combined with 
// merged with 'in-silico damage removed' libraries to improve genotyping

ch_trimmed_formerge = ch_bamutils_decision.notrim
  .mix(ch_trimmed_from_bamutils)
  .groupTuple(by:[0,4,5])
  .map{
        def samplename = it[0]
        def libraryid  = it[1]
        def lane = it[2]
        def seqtype = it[3]
        def organism = it[4]
        def strandedness = it[5]
        def udg = it[6]     
        def bam = it[7].flatten()
        def bai = it[8].flatten()

      [samplename, libraryid, lane, seqtype, organism, strandedness, udg, bam, bai ]
  }
  .branch{
    skip_merging: it[7].size() == 1
    merge_me: it[7].size() > 1
  }

//////////////////////////////////////////////////////////////////////////
/* --    POST aDNA BAM MODIFICATION AND FINAL MAPPING STATISTICS     -- */
//////////////////////////////////////////////////////////////////////////

process additional_library_merge {
  label 'sc_tiny'
  tag "${samplename}"
  publishDir "${params.outdir}/merged_bams/additional", mode: params.publish_dir_mode

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_trimmed_formerge.merge_me

  output:
  tuple samplename, val("${samplename}_libmerged"), lane, seqtype, organism, strandedness, udg, path("*_libmerged_rg_add.bam"), path("*_libmerged_rg_add.bam.{bai,csi}") into ch_output_from_trimmerge

  script:
  def size = params.large_ref ? '-c' : ''
  """
  samtools merge ${samplename}_libmerged_add.bam ${bam}
  picard -Xmx${task.memory.toGiga()}g AddOrReplaceReadGroups I=${samplename}_libmerged_add.bam O=${samplename}_libmerged_rg_add.bam RGID=1 RGLB="${samplename}_additionalmerged" RGPL=illumina RGPU=4410 RGSM="${samplename}_additionalmerged" VALIDATION_STRINGENCY=LENIENT
  samtools index ${samplename}_libmerged_rg_add.bam ${size}
  """
}

ch_trimmed_formerge.skip_merging
  .mix(ch_output_from_trimmerge)
  .into{ ch_output_from_bamutils; ch_addlibmerge_for_qualimap; ch_for_sexdeterrmine_prep }

  // General mapping quality statistics for whole reference sequence - e.g. X and % coverage

process qualimap {
    label 'mc_small'
    tag "${samplename}"
    publishDir "${params.outdir}/qualimap", mode: params.publish_dir_mode

    when:
    !params.skip_qualimap

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_addlibmerge_for_qualimap
    file fasta from ch_fasta_for_qualimap.collect()

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*") into ch_qualimap_results

    script:
    def snpcap = params.snpcapture_bed ? "-gff ${params.snpcapture_bed}" : ''
    """
    qualimap bamqc -bam $bam -nt ${task.cpus} -outdir . -outformat "HTML" ${snpcap} --java-mem-size=${task.memory.toGiga()}G
    """
}

/////////////////////////////
/* --    GENOTYPING     -- */
/////////////////////////////

// Reroute files for genotyping; we have to ensure to select lib-merged BAMs, as input channel will also contain the un-merged ones resulting in unwanted multi-sample VCFs
if ( params.run_genotyping && params.genotyping_source == 'raw' ) {
    ch_output_from_bamutils
      .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes; ch_damagemanipulation_for_genotyping_pileupcaller; ch_damagemanipulation_for_genotyping_angsd }

} else if ( params.run_genotyping && params.genotyping_source == "trimmed" && !params.run_trim_bam )  {
    exit 1, "[nf-core/eager] error: Cannot run genotyping with 'trimmed' source without running BAM trimming (--run_trim_bam)! Please check input parameters."

} else if ( params.run_genotyping && params.genotyping_source == "trimmed" && params.run_trim_bam )  {
    ch_output_from_bamutils
        .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes; ch_damagemanipulation_for_genotyping_pileupcaller; ch_damagemanipulation_for_genotyping_angsd }

} else if ( params.run_genotyping && params.genotyping_source == "pmd" && !params.run_pmdtools )  {
    exit 1, "[nf-core/eager] error: Cannot run genotyping with 'pmd' source without running pmdtools (--run_pmdtools)! Please check input parameters."

} else if ( params.run_genotyping && params.genotyping_source == "pmd" && params.run_pmdtools )  {
  ch_output_from_pmdtools
    .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes; ch_damagemanipulation_for_genotyping_pileupcaller; ch_damagemanipulation_for_genotyping_angsd }

} else if ( params.run_genotyping && params.genotyping_source == "rescaled" && params.run_mapdamage_rescaling) {
  ch_output_from_damagerescaling
    .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes; ch_damagemanipulation_for_genotyping_pileupcaller; ch_damagemanipulation_for_genotyping_angsd }

} else if ( params.run_genotyping && params.genotyping_source == "rescaled" && !params.run_mapdamage_rescaling) {
    exit 1, "[nf-core/eager] error: Cannot run genotyping with 'rescaled' source without running damage rescaling (--run_damagescaling)! Please check input parameters."

} else if ( !params.run_genotyping && !params.run_trim_bam && !params.run_pmdtools )  {
    ch_rmdup_for_skipdamagemanipulation
    .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes; ch_damagemanipulation_for_genotyping_pileupcaller; ch_damagemanipulation_for_genotyping_angsd }

} else if ( !params.run_genotyping && !params.run_trim_bam && params.run_pmdtools )  {
    ch_rmdup_for_skipdamagemanipulation
    .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes; ch_damagemanipulation_for_genotyping_pileupcaller; ch_damagemanipulation_for_genotyping_angsd }

} else if ( !params.run_genotyping && params.run_trim_bam && !params.run_pmdtools )  {
    ch_rmdup_for_skipdamagemanipulation
    .into { ch_damagemanipulation_for_skipgenotyping; ch_damagemanipulation_for_genotyping_ug; ch_damagemanipulation_for_genotyping_hc; ch_damagemanipulation_for_genotyping_freebayes; ch_damagemanipulation_for_genotyping_pileupcaller; ch_damagemanipulation_for_genotyping_angsd }

}

// Unified Genotyper - although not-supported, better for aDNA (because HC does de novo assembly which requires higher coverages), and needed for MultiVCFAnalyzer

process genotyping_ug {
  label 'mc_small'
  tag "${samplename}"
  publishDir "${params.outdir}/genotyping", mode: params.publish_dir_mode, pattern: '*{.vcf.gz,.realign.bam,realign.bai}'

  when:
  params.run_genotyping && params.genotyping_tool == 'ug'

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_damagemanipulation_for_genotyping_ug
  file fasta from ch_fasta_for_genotyping_ug.collect()
  file fai from ch_fai_for_ug.collect()
  file dict from ch_dict_for_ug.collect()

  output: 
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*vcf.gz") into ch_ug_for_multivcfanalyzer,ch_ug_for_vcf2genome
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.realign.{bam,bai}") optional true

  script:
  def defaultbasequalities = !params.gatk_ug_defaultbasequalities ? '' : " --defaultBaseQualities ${params.gatk_ug_defaultbasequalities}" 
  def keep_realign = params.gatk_ug_keep_realign_bam ? "samtools index ${samplename}.realign.bam" : "rm ${samplename}.realign.{bam,bai}"
  if (!params.gatk_dbsnp)
    """
    samtools index -b ${bam}
    gatk3 -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
    gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplename}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
    gatk3 -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
    
    $keep_realign
    
    pigz -p ${task.cpus} ${samplename}.unifiedgenotyper.vcf
    """
  else if (params.gatk_dbsnp)
    """
    samtools index ${bam}
    gatk3 -T RealignerTargetCreator -R ${fasta} -I ${bam} -nt ${task.cpus} -o ${samplename}.intervals ${defaultbasequalities}
    gatk3 -T IndelRealigner -R ${fasta} -I ${bam} -targetIntervals ${samplenane}.intervals -o ${samplename}.realign.bam ${defaultbasequalities}
    gatk3 -T UnifiedGenotyper -R ${fasta} -I ${samplename}.realign.bam -o ${samplename}.unifiedgenotyper.vcf -nt ${task.cpus} --dbsnp ${params.gatk_dbsnp} --genotype_likelihoods_model ${params.gatk_ug_genotype_model} -stand_call_conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} -dcov ${params.gatk_downsample} --output_mode ${params.gatk_ug_out_mode} ${defaultbasequalities}
    
    $keep_realign
    
    pigz -p ${task.cpus} ${samplename}.unifiedgenotyper.vcf
    """
}

 // HaplotypeCaller as 'best practise' tool for human DNA in particular 

process genotyping_hc {
  label 'mc_small'
  tag "${samplename}"
  publishDir "${params.outdir}/genotyping", mode: params.publish_dir_mode

  when:
  params.run_genotyping && params.genotyping_tool == 'hc'

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_damagemanipulation_for_genotyping_hc
  file fasta from ch_fasta_for_genotyping_hc.collect()
  file fai from ch_fai_for_hc.collect()
  file dict from ch_dict_for_hc.collect()

  output: 
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*vcf.gz")

  script:
  if (!params.gatk_dbsnp)
    """
    gatk HaplotypeCaller -R ${fasta} -I ${bam} -O ${samplename}.haplotypecaller.vcf -stand-call-conf ${params.gatk_call_conf} --sample-ploidy ${params.gatk_ploidy} --output-mode ${params.gatk_hc_out_mode} --emit-ref-confidence ${params.gatk_hc_emitrefconf}
    pigz -p ${task.cpus} ${samplename}.haplotypecaller.vcf
    """

  else if (params.gatk_dbsnp)
    """
    gatk HaplotypeCaller -R ${fasta} -I ${bam} -O ${samplename}.haplotypecaller.vcf --dbsnp ${params.gatk_dbsnp} -stand-call-conf ${params.gatk_call_conf} --sample_ploidy ${params.gatk_ploidy} --output_mode ${params.gatk_hc_out_mode} --emit-ref-confidence ${params.gatk_hc_emitrefconf}
    pigz -p ${task.cpus} ${samplename}.haplotypecaller.vcf
    """
}

 // Freebayes for 'more efficient/simple' and more generic genotyping (vs HC) 

process genotyping_freebayes {
  label 'mc_small'
  tag "${samplename}"
  publishDir "${params.outdir}/genotyping", mode: params.publish_dir_mode

  when:
  params.run_genotyping && params.genotyping_tool == 'freebayes'

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_damagemanipulation_for_genotyping_freebayes
  file fasta from ch_fasta_for_genotyping_freebayes.collect()
  file fai from ch_fai_for_freebayes.collect()
  file dict from ch_dict_for_freebayes.collect()

  output: 
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*vcf.gz")
  
  script:
  def skip_coverage = "${params.freebayes_g}" == 0 ? "" : "-g ${params.freebayes_g}"
  """
  freebayes -f ${fasta} -p ${params.freebayes_p} -C ${params.freebayes_C} ${skip_coverage} ${bam} > ${samplename}.freebayes.vcf
  pigz -p ${task.cpus} ${samplename}.freebayes.vcf
  """
}


 // Branch channel by strandedness
ch_damagemanipulation_for_genotyping_pileupcaller
  .branch{
      singleStranded: it[5] == "single"
      doubleStranded: it[5] == "double"
  }
  .set{ch_input_for_genotyping_pileupcaller}

 // Create pileupcaller input tuples
ch_input_for_genotyping_pileupcaller.singleStranded
  .groupTuple(by:[5])
  .set {ch_prepped_for_pileupcaller_single}

ch_input_for_genotyping_pileupcaller.doubleStranded
  .groupTuple(by:[5])
  .set {ch_prepped_for_pileupcaller_double}

process genotyping_pileupcaller {
  label 'mc_small'
  tag "${strandedness}"
  publishDir "${params.outdir}/genotyping", mode: params.publish_dir_mode

  when:
  params.run_genotyping && params.genotyping_tool == 'pileupcaller'

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, bam, bai from ch_prepped_for_pileupcaller_double.mix(ch_prepped_for_pileupcaller_single)
  file fasta from ch_fasta_for_genotyping_pileupcaller.collect()
  file fai from ch_fai_for_pileupcaller.collect()
  file dict from ch_dict_for_pileupcaller.collect()
  path(bed) from ch_bed_for_pileupcaller.collect()
  path(snp) from ch_snp_for_pileupcaller.collect().dump(tag: "Pileupcaller SNP file")

  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("pileupcaller.${strandedness}.*") into ch_for_eigenstrat_snp_coverage

  script:
  def use_bed = bed.getName() != 'nf-core_eager_dummy.txt' ? "-l ${bed}" : ''
  def use_snp = snp.getName() != 'nf-core_eager_dummy2.txt' ? "-f ${snp}" : ''

  def transitions_mode = strandedness == "single" ? "" : "${params.pileupcaller_transitions_mode}" == 'SkipTransitions' ? "--skipTransitions" : "${params.pileupcaller_transitions_mode}" == 'TransitionsMissing' ? "--transitionsMissing" : ""
  def caller = "--${params.pileupcaller_method}"
  def ssmode = strandedness == "single" ? "--singleStrandMode" : ""
  def bam_list = bam.flatten().join(" ")
  def sample_names = samplename.flatten().join(",")
  """
  samtools mpileup -B -q 30 -Q 30 ${use_bed} -f ${fasta} ${bam_list} | pileupCaller ${caller} ${ssmode} ${transitions_mode} --sampleNames ${sample_names} ${use_snp} -e pileupcaller.${strandedness}
  """
}

process eigenstrat_snp_coverage {
  label 'mc_tiny'
  tag "${strandedness}"
  publishDir "${params.outdir}/genotyping", mode: params.publish_dir_mode
  
  when:
  params.run_genotyping && params.genotyping_tool == 'pileupcaller'
  
  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*") from ch_for_eigenstrat_snp_coverage.dump(tag:'eigenstrat_input')
  
  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.json") into ch_eigenstrat_snp_cov_for_multiqc
  path("*_eigenstrat_coverage.txt")
  
  script:
  /* 
  The following code block can be swapped in once the eigenstratdatabasetools MultiQC module becomes available.
  """
  eigenstrat_snp_coverage -i pileupcaller.${strandedness} -s ".txt" >${strandedness}_eigenstrat_coverage.txt -j ${strandedness}_eigenstrat_coverage_mqc.json
  """
  */
  """
  eigenstrat_snp_coverage -i pileupcaller.${strandedness} -s ".txt" >${strandedness}_eigenstrat_coverage.txt
  parse_snp_cov.py ${strandedness}_eigenstrat_coverage.txt
  """
}

process genotyping_angsd {
  label 'mc_small'
  tag "${samplename}"
  publishDir "${params.outdir}/genotyping", mode: params.publish_dir_mode

  when:
  params.run_genotyping && params.genotyping_tool == 'angsd'

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(bam), file(bai) from ch_damagemanipulation_for_genotyping_angsd
  file fasta from ch_fasta_for_genotyping_angsd.collect()
  file fai from ch_fai_for_angsd.collect()
  file dict from ch_dict_for_angsd.collect()

  output: 
  path("${samplename}*")
  
  script:
  switch ( "${params.angsd_glmodel}" ) {
    case "samtools":
    angsd_glmodel = "1"; break
    case "gatk":
    angsd_glmodel = "2"; break
    case "soapsnp":
    angsd_glmodel = "3"; break
    case "syk":
    angsd_glmodel = "4"; break
  }

  switch ( "${params.angsd_glformat}" ) {
    case "text":
    angsd_glformat = "4"; break
    case "binary":
    angsd_glformat = "1"; break
    case "beagle":
    angsd_glformat = "2"; break
    case "binary_three":
    angsd_glformat = "3"; break
  }
  
  def angsd_fasta = !params.angsd_createfasta ? '' : params.angsd_fastamethod == 'random' ? '-doFasta 1 -doCounts 1' : '-doFasta 2 -doCounts 1' 
  def angsd_majorminor = params.angsd_glformat != "beagle" ? '' : '-doMajorMinor 1'
  """
  echo ${bam} > bam.filelist
  mkdir angsd
  angsd -bam bam.filelist -nThreads ${task.cpus} -GL ${angsd_glmodel} -doGlF ${angsd_glformat} ${angsd_majorminor} ${angsd_fasta} -out ${samplename}.angsd
  """
}

////////////////////////////////////
/* --    CONSENSUS CALLING     -- */
////////////////////////////////////

// Generate a simple consensus-called FASTA file based on genotype VCF

process vcf2genome {
  label  'mc_small'
  tag "${samplename}"
  publishDir "${params.outdir}/consensus_sequence", mode: params.publish_dir_mode

  when: 
  params.run_vcf2genome

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(vcf) from ch_ug_for_vcf2genome
  file fasta from ch_fasta_for_vcf2genome.collect()

  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.fasta.gz")

  script:
  def out = !params.vcf2genome_outfile ? "${samplename}.fasta" : "${params.vcf2genome_outfile}"
  def fasta_head = !params.vcf2genome_header ? "${samplename}" : "${params.vcf2genome_header}"
  """
  pigz -f -d -p ${task.cpus} *.vcf.gz
  vcf2genome -Xmx${task.memory.toGiga()}g -draft ${out}.fasta -draftname "${fasta_head}" -in ${vcf.baseName} -minc ${params.vcf2genome_minc} -minfreq ${params.vcf2genome_minfreq} -minq ${params.vcf2genome_minq} -ref ${fasta} -refMod ${out}_refmod.fasta -uncertain ${out}_uncertainy.fasta
  pigz -p ${task.cpus} *.fasta 
  pigz -p ${task.cpus} *.vcf
  """
}

// More complex consensus caller with additional filtering functionality (e.g. for heterozygous calls) to generate SNP tables and other things sometimes used in aDNA bacteria studies

// Create input channel for MultiVCFAnalyzer, possibly mixing with pre-made VCFs.
if (!params.additional_vcf_files) {
    ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it[-1] }.collect()
} else {
    ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it [-1] }.collect().mix(ch_extravcfs_for_multivcfanalyzer)
}

process multivcfanalyzer {
  label  'mc_small'
  publishDir "${params.outdir}/multivcfanalyzer", mode: params.publish_dir_mode

  when:
  params.genotyping_tool == 'ug' && params.run_multivcfanalyzer && params.gatk_ploidy.toString() == '2'

  input:
  file vcf from ch_vcfs_for_multivcfanalyzer
  file fasta from ch_fasta_for_multivcfanalyzer

  output:
  file('fullAlignment.fasta.gz')
  file('info.txt.gz')
  file('snpAlignment.fasta.gz')
  file('snpAlignmentIncludingRefGenome.fasta.gz')
  file('snpStatistics.tsv.gz')
  file('snpTable.tsv.gz')
  file('snpTableForSnpEff.tsv.gz')
  file('snpTableWithUncertaintyCalls.tsv.gz')
  file('structureGenotypes.tsv.gz')
  file('structureGenotypes_noMissingData-Columns.tsv.gz')
  file('MultiVCFAnalyzer.json') optional true into ch_multivcfanalyzer_for_multiqc

  script:
  def write_freqs = params.write_allele_frequencies ? "T" : "F"
  """
  gunzip -f *.vcf.gz
  multivcfanalyzer -Xmx${task.memory.toGiga()}g ${params.snp_eff_results} ${fasta} ${params.reference_gff_annotations} . ${write_freqs} ${params.min_genotype_quality} ${params.min_base_coverage} ${params.min_allele_freq_hom} ${params.min_allele_freq_het} ${params.reference_gff_exclude} *.vcf
  pigz -p ${task.cpus} *.tsv *.txt snpAlignment.fasta snpAlignmentIncludingRefGenome.fasta fullAlignment.fasta
  """
 }

////////////////////////////////////////////////////////////
/* --    HUMAN DNA SPECIFIC ADDITIONAL INFORMATION     -- */
////////////////////////////////////////////////////////////

// Mitochondrial to nuclear ratio helps to evaluate quality of tissue sampled

 process mtnucratio {
  label 'sc_small'
  tag "${samplename}"
  publishDir "${params.outdir}/mtnucratio", mode: params.publish_dir_mode

  when: 
  params.run_mtnucratio

  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_rmdup_formtnucratio

  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.mtnucratio")
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.json") into ch_mtnucratio_for_multiqc

  script:
  """
  mtnucratio -Xmx${task.memory.toGiga()}g ${bam} "${params.mtnucratio_header}"
  """
 }

// Human biological sex estimation

// rename to prevent single/double stranded library sample name-based file conflict
process sexdeterrmine_prep {
  label 'sc_small'
  
  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(bam), path(bai) from ch_for_sexdeterrmine_prep
  
  output:
  file "*_{single,double}strand.bam" into ch_prepped_for_sexdeterrmine

  when:
  params.run_sexdeterrmine

  script:
  """
  mv ${bam} ${bam.baseName}_${strandedness}strand.bam
  """

}

// As we collect all files for a single sex_deterrmine run, we DO NOT use the normal input/output tuple
process sexdeterrmine {
    label 'mc_small'
    publishDir "${params.outdir}/sex_determination", mode: params.publish_dir_mode
     
    input:
    path bam from ch_prepped_for_sexdeterrmine.collect()
    path(bed) from ch_bed_for_sexdeterrmine

    output:
    file "SexDet.txt"
    file "*.json" into ch_sexdet_for_multiqc

    when:
    params.run_sexdeterrmine
    
    script:
    def filter = bed.getName() != 'nf-core_eager_dummy.txt' ? "-b $bed" : ''
    """
    ls *.bam >> bamlist.txt
    samtools depth -aa -q30 -Q30 $filter -f bamlist.txt | sexdeterrmine -f bamlist.txt > SexDet.txt
    """
}

// Human DNA nuclear contamination estimation

 process nuclear_contamination{
    label 'sc_small'
    tag "${samplename}"
    publishDir "${params.outdir}/nuclear_contamination", mode: params.publish_dir_mode

    when:
    params.run_nuclear_contamination

    input:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(input), path(bai) from ch_for_nuclear_contamination

    output:
    tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path('*.X.contamination.out') into ch_from_nuclear_contamination

    script:
    """
    samtools index ${input}
    angsd -i ${input} -r ${params.contamination_chrom_name}:5000000-154900000 -doCounts 1 -iCounts 1 -minMapQ 30 -minQ 30 -out ${libraryid}.doCounts
    contamination -a ${libraryid}.doCounts.icnts.gz -h ${projectDir}/assets/angsd_resources/HapMapChrX.gz 2> ${libraryid}.X.contamination.out
    """
 }
 
// As we collect all files for a single print_nuclear_contamination run, we DO NOT use the normal input/output tuple
process print_nuclear_contamination{
    label 'sc_tiny'
    publishDir "${params.outdir}/nuclear_contamination", mode: params.publish_dir_mode

    when:
    params.run_nuclear_contamination

    input:
    path Contam from ch_from_nuclear_contamination.map { it[7] }.collect()

    output:
    file 'nuclear_contamination.txt'
    file 'nuclear_contamination_mqc.json' into ch_nuclear_contamination_for_multiqc

    script:
    """
    print_x_contamination.py ${Contam.join(' ')}
    """
 }

/////////////////////////////////////////////////////////
/* --    METAGENOMICS-SPECIFIC ADDITIONAL STEPS     -- */
/////////////////////////////////////////////////////////

// Low entropy read filter to reduce input sequences of reads that are highly uninformative, and thus reduce runtime/false positives

process metagenomic_complexity_filter {
  label 'mc_small'
  tag "${samplename}"
  publishDir "${params.outdir}/metagenomic_complexity_filter/", mode: params.publish_dir_mode

  when:
  params.metagenomic_complexity_filter
  
  input:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path(fastq) from ch_bam_filtering_for_metagenomic


  output:
  tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*_lowcomplexityremoved.fq.gz") into ch_lowcomplexityfiltered_for_metagenomic
  path("*_bbduk.stats") into ch_metagenomic_complexity_filter_for_multiqc

  script:
  """
  bbduk.sh -Xmx${task.memory.toGiga()}g in=${fastq} threads=${task.cpus} entropymask=f entropy=${params.metagenomic_complexity_entropy} out=${fastq}_lowcomplexityremoved.fq.gz 2> ${fastq}_bbduk.stats
  """

}

// metagenomic complexity filter bypass

if ( params.metagenomic_complexity_filter ) {
  ch_lowcomplexityfiltered_for_metagenomic
    .set{ ch_filtered_for_metagenomic }
} else {
  ch_metagenomic_for_skipentropyfilter
    .set{ ch_filtered_for_metagenomic }
}

// MALT is a super-fast BLAST replacement typically used for pathogen detection or microbiome profiling against large databases, here using off-target reads from mapping

// As we collect all files for a all metagenomic runs, we DO NOT use the normal input/output tuple!
if (params.metagenomic_tool == 'malt') {
  ch_filtered_for_metagenomic
    .set {ch_input_for_metagenomic_malt}

  ch_input_for_metagenomic_kraken = Channel.empty()
} else if (params.metagenomic_tool == 'kraken') {
  ch_filtered_for_metagenomic
    .set {ch_input_for_metagenomic_kraken}

  ch_input_for_metagenomic_malt = Channel.empty()
} else if ( !params.metagenomic_tool ) {
  ch_input_for_metagenomic_malt = Channel.empty()
  ch_input_for_metagenomic_kraken = Channel.empty()

}

// As we collect all files for a single MALT run, we DO NOT use the normal input/output tuple
process malt {
  label 'mc_small'
  publishDir "${params.outdir}/metagenomic_classification/malt", mode: params.publish_dir_mode

  when:
  params.run_metagenomic_screening && params.run_bam_filtering && params.bam_unmapped_type == 'fastq' && params.metagenomic_tool == 'malt'

  input:
  file fastqs from ch_input_for_metagenomic_malt.map { it[7] }.collect()
  file db from ch_db_for_malt

  output:
  path("*.rma6") into ch_rma_for_maltExtract
  path("*.sam.gz") optional true
  path("malt.log") into ch_malt_for_multiqc

  script:
  if ( "${params.malt_min_support_mode}" == "percent" ) {
    min_supp = "-supp ${params.malt_min_support_percent}" 
  } else if ( "${params.malt_min_support_mode}" == "reads" ) {
    min_supp = "-sup ${params.metagenomic_min_support_reads}"
  }
  def sam_out = params.malt_sam_output ? "-a . -f SAM" : ""
  """
  malt-run \
  -J-Xmx${task.memory.toGiga()}g \
  -t ${task.cpus} \
  -v \
  -o . \
  -d ${db} \
  ${sam_out} \
  -id ${params.percent_identity} \
  -m ${params.malt_mode} \
  -at ${params.malt_alignment_mode} \
  -top ${params.malt_top_percent} \
  ${min_supp} \
  -mq ${params.malt_max_queries} \
  --memoryMode ${params.malt_memory_mode} \
  -i ${fastqs.join(' ')} |&tee malt.log
  """
}

// MaltExtract performs aDNA evaluation from the output of MALT (damage patterns, read lengths etc.)

// As we collect all files for a single MALT extract run, we DO NOT use the normal input/output tuple
process maltextract {
  label 'mc_medium'
  publishDir "${params.outdir}/maltextract/", mode: params.publish_dir_mode

  when: 
  params.run_maltextract && params.metagenomic_tool == 'malt'

  input:
  file rma6 from ch_rma_for_maltExtract.collect()
  file taxon_list from ch_taxonlist_for_maltextract
  file ncbifiles from ch_ncbifiles_for_maltextract
  
  output:
  path "results/" type('dir')
  file "results/*_Wevid.json" optional true into ch_hops_for_multiqc 

  script:
  def destack = params.maltextract_destackingoff ? "--destackingOff" : ""
  def downsam = params.maltextract_downsamplingoff ? "--downSampOff" : ""
  def dupremo = params.maltextract_duplicateremovaloff ? "--dupRemOff" : ""
  def matches = params.maltextract_matches ? "--matches" : ""
  def megsum = params.maltextract_megansummary ? "--meganSummary" : ""
  def topaln = params.maltextract_topalignment ?  "--useTopAlignment" : ""
  def ss = params.single_stranded ? "--singleStranded" : ""
  """
  MaltExtract \
  -Xmx${task.memory.toGiga()}g \
  -t ${taxon_list} \
  -i ${rma6.join(' ')} \
  -o results/ \
  -r ${ncbifiles} \
  -p ${task.cpus} \
  -f ${params.maltextract_filter} \
  -a ${params.maltextract_toppercent} \
  --minPI ${params.maltextract_percentidentity} \
  ${destack} \
  ${downsam} \
  ${dupremo} \
  ${matches} \
  ${megsum} \
  ${topaln} \
  ${ss}

  postprocessing.AMPS.r -r results/ -m ${params.maltextract_filter} -t ${task.cpus} -n ${taxon_list} -j
  """
}

// Kraken is offered as a replacement for MALT as MALT is _very_ resource hungry

if (params.run_metagenomic_screening && params.database.endsWith(".tar.gz") && params.metagenomic_tool == 'kraken'){
  comp_kraken = file(params.database)

  process decomp_kraken {
    input:
    path(ckdb) from comp_kraken
    
    output:
    path(dbname) into ch_krakendb
    
    script:
    dbname = ckdb.toString() - '.tar.gz'
    """
    tar xvzf $ckdb
    mkdir -p $dbname
    mv *.k2d $dbname || echo "nothing to do"
    """
  }

} else if (params.database && ! params.database.endsWith(".tar.gz") && params.run_metagenomic_screening && params.metagenomic_tool == 'kraken') {
    ch_krakendb = Channel.fromPath(params.database).first()
} else {
    ch_krakendb = Channel.empty()
}

process kraken {
  tag "$prefix"
  label 'mc_huge'
  publishDir "${params.outdir}/metagenomic_classification/kraken", mode: params.publish_dir_mode

  when:
  params.run_metagenomic_screening && params.run_bam_filtering && params.bam_unmapped_type == 'fastq' && params.metagenomic_tool == 'kraken'

  input:
  path(fastq) from ch_input_for_metagenomic_kraken.map { it[7] }
  path(krakendb) from ch_krakendb

  output:
  file "*.kraken.out" into ch_kraken_out
  tuple prefix, path("*.kraken2_report") into ch_kraken_report, ch_kraken_for_multiqc

  script:
  prefix = fastq.toString().tokenize('.')[0]
  out = prefix+".kraken.out"
  kreport = prefix+".kraken2_report"
  kreport_old = prefix+".kreport"

  """
  kraken2 --db ${krakendb} --threads ${task.cpus} --output $out --report-minimizer-data --report $kreport $fastq
  cut -f1-3,6-8 $kreport > $kreport_old
  """
}

process kraken_parse {
  tag "$name"
  errorStrategy 'ignore'

  input:
  tuple val(name), path(kraken_r) from ch_kraken_report

  output:
  path('*_kraken_parsed.csv') into ch_kraken_parsed

  script:
  read_out = name+".read_kraken_parsed.csv"
  kmer_out =  name+".kmer_kraken_parsed.csv"
  """
  kraken_parse.py -c ${params.metagenomic_min_support_reads} -or $read_out -ok $kmer_out $kraken_r
  """    
}

process kraken_merge {
  publishDir "${params.outdir}/metagenomic_classification/kraken", mode: params.publish_dir_mode

  input:
  file csv_count from ch_kraken_parsed.collect()

  output:
  path('*.csv')

  script:
  read_out = "kraken_read_count.csv"
  kmer_out = "kraken_kmer_duplication.csv"
  """
  merge_kraken_res.py -or $read_out -ok $kmer_out
  """    
}

//////////////////////////////////////
/* --    PIPELINE COMPLETION     -- */
//////////////////////////////////////

// Pipeline documentation for on-server guidance

process output_documentation {
    label 'sc_tiny'
    publishDir "${params.outdir}/documentation", mode: params.publish_dir_mode

    input:
    file output_docs from ch_output_docs
    file images from ch_output_docs_images

    output:
    file "results_description.html"

    script:
    """
    markdown_to_html.py $output_docs -o results_description.html
    """
}

/*
 * Parse software version numbers
 */

process get_software_versions {
  label 'mc_small'
    publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode,
        saveAs: { filename ->
                      if (filename.indexOf(".csv") > 0) filename
                      else null
                }

    output:
    file 'software_versions_mqc.yaml' into software_versions_yaml
    file "software_versions.csv"

    script:
    """
    echo $workflow.manifest.version &> v_pipeline.txt
    echo $workflow.nextflow.version &> v_nextflow.txt
    
    fastqc --version &> v_fastqc.txt 2>&1 || true
    AdapterRemoval --version  &> v_adapterremoval.txt 2>&1 || true
    fastp --version &> v_fastp.txt 2>&1 || true
    bwa &> v_bwa.txt 2>&1 || true
    circulargenerator --help | head -n 1 &> v_circulargenerator.txt 2>&1 || true
    samtools --version &> v_samtools.txt 2>&1 || true
    dedup -v &> v_dedup.txt 2>&1 || true
    ## bioconda recipe of picard is incorrectly set up and extra warning made with stderr, this ugly command ensures only version exported
    ( exec 7>&1; picard MarkDuplicates --version 2>&1 >&7 | grep -v '/' >&2 ) 2> v_markduplicates.txt || true
    qualimap --version &> v_qualimap.txt 2>&1 || true
    preseq &> v_preseq.txt 2>&1 || true
    gatk --version 2>&1 | head -n 1 > v_gatk.txt 2>&1 || true
    gatk3 --version 2>&1 > v_gatk3.txt 2>&1 || true
    freebayes --version &> v_freebayes.txt 2>&1 || true
    bedtools --version &> v_bedtools.txt 2>&1 || true
    damageprofiler --version &> v_damageprofiler.txt 2>&1 || true
    bam --version &> v_bamutil.txt 2>&1 || true
    pmdtools --version &> v_pmdtools.txt 2>&1 || true
    angsd -h |& head -n 1 | cut -d ' ' -f3-4 &> v_angsd.txt 2>&1 || true 
    multivcfanalyzer --help | head -n 1 &> v_multivcfanalyzer.txt 2>&1 || true
    malt-run --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' &> v_malt.txt 2>&1 || true
    MaltExtract --help | head -n 2 | tail -n 1 &> v_maltextract.txt 2>&1 || true
    multiqc --version &> v_multiqc.txt 2>&1 || true
    vcf2genome -h |& head -n 1 &> v_vcf2genome.txt || true
    mtnucratio --help &> v_mtnucratiocalculator.txt || true
    sexdeterrmine --version &> v_sexdeterrmine.txt || true
    kraken2 --version | head -n 1 &> v_kraken.txt || true
    endorS.py --version &> v_endorSpy.txt || true
    pileupCaller --version &> v_sequencetools.txt 2>&1 || true
    bowtie2 --version | grep -a 'bowtie2-.* -fdebug' > v_bowtie2.txt || true
    eigenstrat_snp_coverage --version | cut -d ' ' -f2 >v_eigenstrat_snp_coverage.txt || true
    mapDamage --version > v_mapdamage.txt || true
    bbduk.sh | grep 'Last modified' | cut -d' ' -f 3-99 > v_bbduk.txt || true

    scrape_software_versions.py &> software_versions_mqc.yaml
    """
}

// MultiQC file generation for pipeline report
//def workflow_summary = NfcoreSchema.params_summary_multiqc(workflow, summary_params)

//ch_workflow_summary = Channel.value(workflow_summary)

process multiqc {
    label 'sc_medium'

    publishDir "${params.outdir}/multiqc", mode: params.publish_dir_mode

    input:
    file multiqc_config from ch_multiqc_config
    file (mqc_custom_config) from ch_multiqc_custom_config.collect().ifEmpty([])
    file software_versions_mqc from software_versions_yaml.collect().ifEmpty([])
    file logo from ch_eager_logo
    file ('fastqc_raw/*') from ch_prefastqc_for_multiqc.collect().ifEmpty([])
    path('fastqc/*') from ch_fastqc_after_clipping.collect().ifEmpty([])
    file ('adapter_removal/*') from ch_adapterremoval_logs.collect().ifEmpty([])
    file ('mapping/bt2/*') from ch_bt2_for_multiqc.collect().ifEmpty([])
    file ('flagstat/*') from ch_flagstat_for_multiqc.collect().ifEmpty([])
    file ('flagstat_filtered/*') from ch_bam_filtered_flagstat_for_multiqc.collect().ifEmpty([])
    file ('preseq/*') from ch_preseq_for_multiqc.collect().ifEmpty([])
    file ('damageprofiler/dmgprof*/*') from ch_damageprofiler_results.collect().ifEmpty([])
    file ('qualimap/qualimap*/*') from ch_qualimap_results.collect().ifEmpty([])
    file ('markdup/*') from ch_markdup_results_for_multiqc.collect().ifEmpty([])
    file ('dedup*/*') from ch_dedup_results_for_multiqc.collect().ifEmpty([])
    file ('fastp/*') from ch_fastp_for_multiqc.collect().ifEmpty([])
    file ('sexdeterrmine/*') from ch_sexdet_for_multiqc.collect().ifEmpty([])
    file ('mutnucratio/*') from ch_mtnucratio_for_multiqc.collect().ifEmpty([])
    file ('endorspy/*') from ch_endorspy_for_multiqc.collect().ifEmpty([])
    file ('multivcfanalyzer/*') from ch_multivcfanalyzer_for_multiqc.collect().ifEmpty([])
    file ('fastp_lowcomplexityfilter/*') from ch_metagenomic_complexity_filter_for_multiqc.collect().ifEmpty([])
    file ('malt/*') from ch_malt_for_multiqc.collect().ifEmpty([])
    file ('kraken/*') from ch_kraken_for_multiqc.collect().ifEmpty([])
    file ('hops/*') from ch_hops_for_multiqc.collect().ifEmpty([])
    file ('nuclear_contamination/*') from ch_nuclear_contamination_for_multiqc.collect().ifEmpty([])
    file ('genotyping/*') from ch_eigenstrat_snp_cov_for_multiqc.collect().ifEmpty([])
    file workflow_summary from ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml")

    output:
    file "*multiqc_report.html" into ch_multiqc_report
    file "*_data"

    script:
    rtitle = ''
    rfilename = ''
    if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
        rtitle = "--title \"${workflow.runName}\""
        rfilename = "--filename " + workflow.runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report"
    }
    
    def custom_config_file = params.multiqc_config ? "--config $mqc_custom_config" : ''
    """
    multiqc -f $rtitle $rfilename $multiqc_config $custom_config_file .
    """
}

// Send completion emails if requested, so user knows data is ready

workflow.onComplete {

    // Set up the e-mail variables
    def subject = "[nf-core/eager] Successful: $workflow.runName"
    if (!workflow.success) {
        subject = "[nf-core/eager] FAILED: $workflow.runName"
    }
    def email_fields = [:]
    email_fields['version'] = workflow.manifest.version
    email_fields['runName'] = workflow.runName
    email_fields['success'] = workflow.success
    email_fields['dateComplete'] = workflow.complete
    email_fields['duration'] = workflow.duration
    email_fields['exitStatus'] = workflow.exitStatus
    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
    email_fields['errorReport'] = (workflow.errorReport ?: 'None')
    email_fields['commandLine'] = workflow.commandLine
    email_fields['projectDir'] = workflow.projectDir
    email_fields['summary'] = summary
    email_fields['summary']['Date Started'] = workflow.start
    email_fields['summary']['Date Completed'] = workflow.complete
    email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
    email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
    if (workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
    if (workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
    if (workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
    email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
    email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
    email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp

    // On success try attach the multiqc report
    def mqc_report = null
    try {
        if (workflow.success) {
            mqc_report = ch_multiqc_report.getVal()
            if (mqc_report.getClass() == ArrayList) {
                log.warn "[nf-core/eager] Found multiple reports from process 'multiqc', will use only one"
                mqc_report = mqc_report[0]
            }
        }
    } catch (all) {
        log.warn "[nf-core/eager] Could not attach MultiQC report to summary email"
    }

    // Check if we are only sending emails on failure
    email_address = params.email
    if (!params.email && params.email_on_fail && !workflow.success) {
        email_address = params.email_on_fail
    }

    // Render the TXT template
    def engine = new groovy.text.GStringTemplateEngine()
    def tf = new File("$projectDir/assets/email_template.txt")
    def txt_template = engine.createTemplate(tf).make(email_fields)
    def email_txt = txt_template.toString()

    // Render the HTML template
    def hf = new File("$projectDir/assets/email_template.html")
    def html_template = engine.createTemplate(hf).make(email_fields)
    def email_html = html_template.toString()

    // Render the sendmail template
    def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.max_multiqc_email_size.toBytes() ]
    def sf = new File("$projectDir/assets/sendmail_template.txt")
    def sendmail_template = engine.createTemplate(sf).make(smail_fields)
    def sendmail_html = sendmail_template.toString()

    // Send the HTML e-mail
    if (email_address) {
        try {
            if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
            // Try to send HTML e-mail using sendmail
            [ 'sendmail', '-t' ].execute() << sendmail_html
            log.info "[nf-core/eager] Sent summary e-mail to $email_address (sendmail)"
        } catch (all) {
            // Catch failures and try with plaintext
            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
            if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
              mail_cmd += [ '-A', mqc_report ]
            }
            mail_cmd.execute() << email_html
            log.info "[nf-core/eager] Sent summary e-mail to $email_address (mail)"
        }
    }

    // Write summary e-mail HTML to a file
    def output_d = new File("${params.outdir}/pipeline_info/")
    if (!output_d.exists()) {
        output_d.mkdirs()
    }
    def output_hf = new File(output_d, "pipeline_report.html")
    output_hf.withWriter { w -> w << email_html }
    def output_tf = new File(output_d, "pipeline_report.txt")
    output_tf.withWriter { w -> w << email_txt }

    c_green = params.monochrome_logs ? '' : "\033[0;32m";
    c_purple = params.monochrome_logs ? '' : "\033[0;35m";
    c_red = params.monochrome_logs ? '' : "\033[0;31m";
    c_reset = params.monochrome_logs ? '' : "\033[0m";

    if (workflow.stats.ignoredCount > 0 && workflow.success) {
        log.info "-${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}-"
        log.info "-${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}-"
        log.info "-${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}-"
    }

    if (workflow.success) {
        log.info "-${c_purple}[nf-core/eager]${c_green} Pipeline completed successfully${c_reset}-"
        log.info "-${c_purple}[nf-core/eager]${c_green} MultiQC run report can be found in ${params.outdir}/multiqc ${c_reset}-"
    } else {
        checkHostname()
        log.info "-${c_purple}[nf-core/eager]${c_red} Pipeline completed with errors${c_reset}-"
    }

}

workflow.onError {
    // Print unexpected parameters - easiest is to just rerun validation
    NfcoreSchema.validateParameters(params, json_schema, log)
}


/////////////////////////////////////
/* --    AUXILARY FUNCTIONS     -- */
/////////////////////////////////////

// Channelling the TSV file containing FASTQ or BAM 
def extract_data(tsvFile) {
    Channel.fromPath(tsvFile)
        .splitCsv(header: true, sep: '\t')
        .dump(tag:'tsv_extract')
        .map { row ->

            def expected_keys = ['Sample_Name', 'Library_ID', 'Lane', 'Colour_Chemistry', 'SeqType', 'Organism', 'Strandedness', 'UDG_Treatment', 'R1', 'R2', 'BAM']
            if ( !row.keySet().containsAll(expected_keys) ) exit 1, "[nf-core/eager] error: Invalid TSV input - malformed column names. Please check input TSV. Column names should be: ${expected_keys.join(", ")}"

            checkNumberOfItem(row, 11)

            if ( row.Sample_Name == null || row.Sample_Name.isEmpty() ) exit 1, "[nf-core/eager] error: the Sample_Name column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.Library_ID == null || row.Library_ID.isEmpty() ) exit 1, "[nf-core/eager] error: the Library_ID column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.Lane == null || row.Lane.isEmpty() ) exit 1, "[nf-core/eager] error: the Lane column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.Colour_Chemistry == null || row.Colour_Chemistry.isEmpty() ) exit 1, "[nf-core/eager] error: the Colour_Chemistry column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.SeqType == null || row.SeqType.isEmpty() ) exit 1, "[nf-core/eager] error: the SeqType column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.Organism == null || row.Organism.isEmpty() ) exit 1, "[nf-core/eager] error: the Organism column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.Strandedness == null || row.Strandedness.isEmpty() ) exit 1, "[nf-core/eager] error: the Strandedness column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.UDG_Treatment == null || row.UDG_Treatment.isEmpty() ) exit 1, "[nf-core/eager] error: the UDG_Treatment column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.R1 == null || row.R1.isEmpty() ) exit 1, "[nf-core/eager] error: the R1 column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.R2 == null || row.R2.isEmpty() ) exit 1, "[nf-core/eager] error: the R2 column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
            if ( row.BAM == null || row.BAM.isEmpty() ) exit 1, "[nf-core/eager] error: the BAM column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"

            def samplename = row.Sample_Name
            def libraryid  = row.Library_ID
            def lane = row.Lane
            def colour = row.Colour_Chemistry
            def seqtype = row.SeqType
            def organism = row.Organism
            def strandedness = row.Strandedness
            def udg = row.UDG_Treatment
            def r1 = row.R1.matches('NA') ? 'NA' : return_file(row.R1)
            def r2 = row.R2.matches('NA') ? 'NA' : return_file(row.R2)
            def bam = row.BAM.matches('NA') ? 'NA' : return_file(row.BAM)

            // check no empty metadata fields
            if (samplename == '' || libraryid == '' || lane == '' || colour == '' || seqtype == '' || organism == '' || strandedness == '' || udg == '' || r1 == '' || r2 == '' || bam == '') exit 1, "[nf-core/eager] error: a field/column does not contain any information. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"

            // Check no 'empty' rows
            if (r1.matches('NA') && r2.matches('NA') && bam.matches('NA')) exit 1, "[nf-core/eager] error: A row in your TSV appears to have all files defined as NA. See '--help' flag and documentation under 'running the pipeline' for more information. Check row for: ${samplename}"

            // Ensure BAMs aren't submitted with PE
            if (!bam.matches('NA') && seqtype.matches('PE')) exit 1, "[nf-core/eager] error: BAM input rows in TSV cannot be set as PE, only SE. See '--help' flag and documentation under 'running the pipeline' for more information. Check row for: ${samplename}"

            // Check valid UDG treatment
            if (!udg.matches('none') && !udg.matches('half') && !udg.matches('full')) exit 1, "[nf-core/eager] error: UDG treatment can only be 'none', 'half' or 'full'. See '--help' flag and documentation under 'running the pipeline' for more information. You have '${udg}'"

            // Check valid colour chemistry
            if (!colour.matches('2') && !colour.matches('4')) exit 1, "[nf-core/eager] error: Colour chemistry in TSV can either be 2 (e.g. NextSeq/NovaSeq) or 4 (e.g. HiSeq/MiSeq)"

            //  Ensure that we do not accept incompatible chemistry setup
            if (!seqtype.matches('PE') && !seqtype.matches('SE')) exit 1, "[nf-core/eager] error:  SeqType for one or more rows in TSV is neither SE nor PE! see '--help' flag and documentation under 'running the pipeline' for more information. You have: '${seqtype}'"
            
           // So we don't accept existing files that are wrong format: e.g. fasta or sam
            if ( !r1.matches('NA') && !has_extension(r1, "fastq.gz") && !has_extension(r1, "fq.gz") && !has_extension(r1, "fastq") && !has_extension(r1, "fq")) exit 1, "[nf-core/eager] error: A specified R1 file either has a non-recognizable FASTQ extension or is not NA. See '--help' flag and documentation under 'running the pipeline' for more information. Check: ${r1}"
            if ( !r2.matches('NA') && !has_extension(r2, "fastq.gz") && !has_extension(r2, "fq.gz") && !has_extension(r2, "fastq") && !has_extension(r2, "fq")) exit 1, "[nf-core/eager] error: A specified R2 file either has a non-recognizable FASTQ extension or is not NA. See '--help' flag and documentation under 'running the pipeline' for more information. Check: ${r2}"
            if ( !bam.matches('NA') && !has_extension(bam, "bam")) exit 1, "[nf-core/eager] error: A specified R1 file either has a non-recognizable BAM extension or is not NA. See '--help' flag and documentation under 'running the pipeline' for more information. Check: ${bam}"
            
            [ samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, r1, r2, bam ]

        }

    }

// Check if a row has the expected number of item
def checkNumberOfItem(row, number) {
    if (row.size() != number) exit 1, "[nf-core/eager] error:  Invalid TSV input - malformed row (e.g. missing column) in ${row}, see '--help' flag and documentation under 'running the pipeline' for more information"
    return true
}

// Return file if it exists
def return_file(it) {
    if (!file(it).exists()) exit 1, "[nf-core/eager] error: Cannot find supplied FASTQ or BAM input file. If using input method TSV set to NA if no file required. See '--help' flag and documentation under 'running the pipeline' for more information. Check file: ${it}" 
    return file(it)
}

// Check file extension
def has_extension(it, extension) {
    it.toString().toLowerCase().endsWith(extension.toLowerCase())
}

// Extract FastQs from Path
// Create a channel of FASTQs from a directory pattern: "my_samples/*/"
// All FASTQ files in subdirectories are collected and emitted;
// they must have _R1_ and/or _R2_ in their names.
def retrieve_input_paths(input, colour_chem, pe_se, ds_ss, udg_treat, bam_in) {

  if ( !bam_in ) {
        if( pe_se ) {
            log.info "Generating single-end FASTQ data TSV"
            Channel
                .fromFilePairs( input, size: 1 )
                .filter { it =~/.*.fastq.gz|.*.fq.gz|.*.fastq|.*.fq/ }
                .ifEmpty { exit 1, "[nf-core/eager] error:  Your specified FASTQ read files did not end in: '.fastq.gz', '.fq.gz', '.fastq', or '.fq'. Did you forget --bam?" }
                .map { row -> [ row[0], [ row[1][0] ] ] }
                .ifEmpty { exit 1, "[nf-core/eager] error:  --input was empty - no input files supplied!" }
                .into { ch_reads_for_faketsv; ch_reads_for_validate }

                // Check we don't have any duplicated sample names due to fromFilePairs behaviour of calculating sample name from anything before R1/R2 glob
                ch_reads_for_validate
                  .groupTuple()
                  .map{
                    if ( validate_size(it[1], 1) ) { null } else { exit 1, "[nf-core/eager] error: You have supplied non-unique sample names (text before R1/R2 indication). Did you accidentally supply paired-end data?  see '--help' flag and documentation under 'running the pipeline' for more information. Check duplicates of: ${it[0]}" } 
                  }

        } else if (!pe_se ){
            log.info "Generating paired-end FASTQ data TSV"

            Channel
                .fromFilePairs( input )
                .filter { it =~/.*.fastq.gz|.*.fq.gz|.*.fastq|.*.fq/ }
                .ifEmpty { exit 1, "[nf-core/eager] error: Files could not be found. Do the specified FASTQ read files end in: '.fastq.gz', '.fq.gz', '.fastq', or '.fq'? Did you forget --single_end?" }
                .map { row -> [ row[0], [ row[1][0], row[1][1] ] ] }
                .ifEmpty { exit 1, "[nf-core/eager] error: --input was empty - no input files supplied!" }
                .into { ch_reads_for_faketsv; ch_reads_for_validate }

                // Check we don't have any duplicated sample names due to fromFilePairs behaviour of calculating sample name from anything before R1/R2 glob
                ch_reads_for_validate
                  .groupTuple()
                  .map{
                    if ( validate_size(it[1], 1) ) { null } else { exit 1, "[nf-core/eager] error: You have supplied non-unique sample names (text before R1/R2 indication). See '--help' flag and documentation under 'running the pipeline' for more information. Check duplicates of: ${it[0]}" } 
                  }

        } 

    } else if ( bam_in ) {
              log.info "Generating BAM data TSV"

         Channel
            .fromFilePairs( input, size: 1 )
            .filter { it =~/.*.bam/ }
            .map { row -> [ row[0], [ row[1][0] ] ] }
            .ifEmpty { exit 1, "[nf-core/eager] error: Cannot find any bam file matching: ${input}" }
            .set { ch_reads_for_faketsv }

    }

ch_reads_for_faketsv
  .map{

      def samplename = it[0]
      def libraryid  = it[0]
      def lane = 0
      def colour = "${colour_chem}"
      def seqtype = pe_se ? 'SE' : 'PE'
      def organism = 'NA'
      def strandedness = ds_ss ? 'single' : 'double'
      def udg = udg_treat
      def r1 = !bam_in ? return_file(it[1][0]) : 'NA'
      def r2 = !bam_in && !pe_se ? return_file(it[1][1]) : 'NA'
      def bam = bam_in && pe_se ? return_file(it[1][0]) : 'NA'

      [ samplename, libraryid, lane, colour, seqtype, organism, strandedness, udg, r1, r2, bam ]
  }
  .ifEmpty {exit 1, "[nf-core/eager] error: Invalid file paths with --input"}

}

// Function to check length of collection in a channel closure is as expected (e.g. with .map())
def validate_size(collection, size){
    if ( collection.size() != size ) { return false } else { return true }
}

def checkHostname() {
    def c_reset = params.monochrome_logs ? '' : "\033[0m"
    def c_white = params.monochrome_logs ? '' : "\033[0;37m"
    def c_red = params.monochrome_logs ? '' : "\033[1;91m"
    def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
    if (params.hostnames) {
        def hostname = 'hostname'.execute().text.trim()
        params.hostnames.each { prof, hnames ->
            hnames.each { hname ->
                if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
                    log.error "${c_red}====================================================${c_reset}\n" +
                            "  ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" +
                            "  but your machine hostname is ${c_white}'$hostname'${c_reset}\n" +
                            "  ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" +
                            "${c_red}====================================================${c_reset}\n"
                }
            }
        }
    }
}