Adds Bowtie2 to address

docs/output.md

@@ -475,7 +475,7 @@ This plot shows the distirbution of th frequency of reads at different GC conten
 Things to watch out for:
 
 - This plot should normally show a normal distribution around the average GC content of your reference genome.
-- Binomial peaks may represent lab-based artefacts that should be further investigated.
+- Bimodal peaks may represent lab-based artefacts that should be further investigated.
 - Skews of the peak to a higher GC content that the reference in Illumina dual-colour chemistry data (e.g. NextSeq or NovaSeq), may suggest long poly-G tails that are mapping to poly-G stretches of your genome. The EAGER2 trimming option `--complexity_filter_poly_g` can be used to remove these tails by utilising the tool FastP for detection and trimming.
 
 ## Output Files

docs/usage.md

@@ -10,183 +10,30 @@
   - [Running the pipeline](#running-the-pipeline)
     - [Updating the pipeline](#updating-the-pipeline)
     - [Mandatory Arguments](#mandatory-arguments)
-      - [`-profile`](#-profile)
-      - [`--input`](#--input)
-        - [Direct Input Method](#direct-input-method)
-        - [TSV Input Method](#tsv-input-method)
-      - [`--bam`](#--bam)
-      - [`--single_stranded`](#--single_stranded)
-      - [`--colour_chemistry`](#--colour_chemistry)
-      - [`--fasta`](#--fasta)
-      - [`--genome` (using iGenomes)](#--genome-using-igenomes)
     - [Output Directories](#output-directories)
-      - [`--outdir`](#--outdir)
-      - [`-w / -work-dir`](#-w---work-dir)
     - [Optional Reference Options](#optional-reference-options)
-      - [`--large_ref`](#--large_ref)
-      - [`--save_reference`](#--save_reference)
-      - [`--bwa_index`](#--bwa_index)
-      - [`--seq_dict`](#--seq_dict)
-      - [`--fasta_index`](#--fasta_index)
     - [Other run specific parameters](#other-run-specific-parameters)
-      - [`-r`](#-r)
-      - [`--max_memory`](#--max_memory)
-      - [`--max_time`](#--max_time)
-      - [`--max_cpus`](#--max_cpus)
-      - [`--email`](#--email)
-      - [`--plaintext_email`](#--plaintext_email)
-      - [`-name`](#-name)
-      - [`-resume`](#-resume)
-      - [`-c`](#-c)
-      - [`--monochrome_logs`](#--monochrome_logs)
-      - [`--multiqc_config`](#--multiqc_config)
-      - [`--custom_config_version`](#--custom_config_version)
   - [Adjustable parameters for nf-core/eager](#adjustable-parameters-for-nf-coreeager)
     - [Step skipping parameters](#step-skipping-parameters)
-      - [`--skip_fastqc`](#--skip_fastqc)
-      - [`--skip_adapterremoval`](#--skip_adapterremoval)
-      - [`--skip_preseq`](#--skip_preseq)
-      - [`--skip_deduplication`](#--skip_deduplication)
-      - [`--skip_damage_calculation`](#--skip_damage_calculation)
-      - [`--skip_qualimap`](#--skip_qualimap)
     - [BAM Conversion Options](#bam-conversion-options)
-      - [`--run_convertinputbam`](#--run_convertinputbam)
     - [Complexity Filtering Options](#complexity-filtering-options)
-      - [`--complexity_filter_poly_g`](#--complexity_filter_poly_g)
-      - [`--complexity_filter_poly_g_min`](#--complexity_filter_poly_g_min)
     - [Adapter Clipping and Merging Options](#adapter-clipping-and-merging-options)
-      - [`--clip_forward_adaptor`](#--clip_forward_adaptor)
-      - [`--clip_reverse_adaptor`](#--clip_reverse_adaptor)
-      - [`--clip_readlength](#--clip_readlength)
-      - [`--clip_min_read_quality`](#--clip_min_read_quality)
-      - [`--clip_min_adap_overlap`](#--clip_min_adap_overlap)
-      - [`--skip_collapse`](#--skip_collapse)
-      - [`--skip_trim`](#--skip_trim)
-      - [`--preserve5p`](#--preserve5p)
-      - [`--mergedonly`](#--mergedonly)
     - [Read Mapping Parameters](#read-mapping-parameters)
-      - [`--mapper`](#--mapper)
-      - [BWA (default)](#bwa-default)
-        - [`--bwaalnn`](#--bwaalnn)
-        - [`--bwaalnk`](#--bwaalnk)
-        - [`--bwaalnl`](#--bwaalnl)
-      - [CircularMapper](#circularmapper)
-        - [`--circularextension`](#--circularextension)
-        - [`--circulartarget`](#--circulartarget)
-        - [`--circularfilter`](#--circularfilter)
-      - [Bowtie2](#bowtie2)
-        - [`--bt2_alignmode`](#--bt2_alignmode)
-        - [`--bt2_sensitivity`](#--bt2_sensitivity)
-        - [`--bt2n`](#--bt2n)
-        - [`--bt2l`](#--bt2l)
-        - [`-bt2_trim5`](#-bt2_trim5)
-        - [`-bt2_trim3`](#-bt2_trim3)
     - [Mapped Reads Stripping](#mapped-reads-stripping)
-      - [`--strip_input_fastq`](#--strip_input_fastq)
-      - [`--strip_mode`](#--strip_mode)
     - [Read Filtering and Conversion Parameters](#read-filtering-and-conversion-parameters)
-      - [`--run_bam_filtering`](#--run_bam_filtering)
-      - [`--bam_discard_unmapped`](#--bam_discard_unmapped)
-      - [`--bam_unmapped_type`](#--bam_unmapped_type)
-      - [`--bam_mapping_quality_threshold`](#--bam_mapping_quality_threshold)
     - [Read DeDuplication Parameters](#read-deduplication-parameters)
-      - [`--dedupper`](#--dedupper)
-      - [`--dedup_all_merged`](#--dedup_all_merged)
     - [Library Complexity Estimation Parameters](#library-complexity-estimation-parameters)
-      - [`--preseq_step_size`](#--preseq_step_size)
     - [DNA Damage Assessment Parameters](#dna-damage-assessment-parameters)
-      - [`--udg_type`](#--udg_type)
-      - [`--damageprofiler_length`](#--damageprofiler_length)
-      - [`--damageprofiler_threshold`](#--damageprofiler_threshold)
-      - [`--damageprofiler_yaxis`](#--damageprofiler_yaxis)
-      - [`--run_pmdtools`](#--run_pmdtools)
-      - [`--pmdtools_range`](#--pmdtools_range)
-      - [`--pmdtools_threshold`](#--pmdtools_threshold)
-      - [`--pmdtools_reference_mask`](#--pmdtools_reference_mask)
-      - [`--pmdtools_max_reads`](#--pmdtools_max_reads)
     - [BAM Trimming Parameters](#bam-trimming-parameters)
-      - [`--run_trim_bam`](#--run_trim_bam)
-      - [`--bamutils_clip_left` / `--bamutils_clip_right`](#--bamutils_clip_left----bamutils_clip_right)
-      - [`--bamutils_softclip`](#--bamutils_softclip)
     - [Captured Library Parameters](#captured-library-parameters)
-      - [`--snpcapture` false](#--snpcapture-false)
-      - [`--bedfile`](#--bedfile)
     - [Feature Annotation Statistics](#feature-annotation-statistics)
-      - [`--run_bedtools_coverage`](#--run_bedtools_coverage)
-      - [`--anno_file`](#--anno_file)
     - [Genotyping Parameters](#genotyping-parameters)
-      - [`--run_genotyping`](#--run_genotyping)
-      - [`--genotyping_tool`](#--genotyping_tool)
-      - [`--genotyping_source`](#--genotyping_source)
-      - [`--gatk_ug_jar`](#--gatk_ug_jar)
-      - [`--gatk_call_conf`](#--gatk_call_conf)
-      - [`--gatk_ploidy`](#--gatk_ploidy)
-      - [`--gatk_dbsnp`](#--gatk_dbsnp)
-      - [`--gatk_ug_out_mode`](#--gatk_ug_out_mode)
-      - [`--gatk_hc_out_mode`](#--gatk_hc_out_mode)
-      - [`--gatk_ug_genotype_model`](#--gatk_ug_genotype_model)
-      - [`--gatk_hc_emitrefconf`](#--gatk_hc_emitrefconf)
-      - [`--gatk_ug_keep_realign_bam`](#--gatk_ug_keep_realign_bam)
-      - [`--gatk_downsample`](#--gatk_downsample)
-      - [`--gatk_ug_gatk_ug_defaultbasequalities`](#--gatk_ug_gatk_ug_defaultbasequalities)
-      - [`--freebayes_C`](#--freebayes_c)
-      - [`--freebayes_g`](#--freebayes_g)
-      - [`--freebayes_p`](#--freebayes_p)
-      - [`--pileupcaller_bedfile`](#--pileupcaller_bedfile)
-      - [`--pileupcaller_snpfile`](#--pileupcaller_snpfile)
-      - [`--pileupcaller_method`](#--pileupcaller_method)
     - [Consensus Sequence Generation](#consensus-sequence-generation)
-      - [`--run_vcf2genome`](#--run_vcf2genome)
-      - [`--vcf2genome_outfile`](#--vcf2genome_outfile)
-      - [`--vcf2genome_header`](#--vcf2genome_header)
-      - [`--vcf2genome_minc`](#--vcf2genome_minc)
-      - [`--vcf2genome_minq`](#--vcf2genome_minq)
-      - [`--vcf2genome_minfreq`](#--vcf2genome_minfreq)
     - [Mitochondrial to Nuclear Ratio](#mitochondrial-to-nuclear-ratio)
-      - [`--run_mtnucratio`](#--run_mtnucratio)
-      - [`--mtnucratio_header`](#--mtnucratio_header)
     - [SNP Table Generation](#snp-table-generation)
-      - [`--run_multivcfanalyzer`](#--run_multivcfanalyzer)
-      - [`--write_allele_frequencies`](#--write_allele_frequencies)
-      - [`--min_genotype_quality`](#--min_genotype_quality)
-      - [`--min_base_coverage`](#--min_base_coverage)
-      - [`--min_allele_freq_hom`](#--min_allele_freq_hom)
-      - [`--min_allele_freq_het`](#--min_allele_freq_het)
-      - [`--additional_vcf_files`](#--additional_vcf_files)
-      - [`--reference_gff_annotations`](#--reference_gff_annotations)
-      - [`--reference_gff_exclude`](#--reference_gff_exclude)
-      - [`--snp_eff_results`](#--snp_eff_results)
     - [Human Sex Determination](#human-sex-determination)
-      - [`--run_sexdeterrmine`](#--run_sexdeterrmine)
-      - [`--sexdeterrmine_bedfile`](#--sexdeterrmine_bedfile)
     - [Human Nuclear Contamination](#human-nuclear-contamination)
-      - [`--run_nuclear_contamination`](#--run_nuclear_contamination)
-      - [`--contamination_chrom_name`](#--contamination_chrom_name)
     - [Metagenomic Screening](#metagenomic-screening)
-      - [`--run_metagenomic_screening`](#--run_metagenomic_screening)
-      - [`--metagenomic_tool`](#--metagenomic_tool)
-      - [`--metagenomic_min_support_reads`](#--metagenomic_min_support_reads)
-      - [`--database`](#--database)
-      - [`--percent_identity`](#--percent_identity)
-      - [`--malt_mode`](#--malt_mode)
-      - [`--malt_alignment_mode`](#--malt_alignment_mode)
-      - [`--malt_top_percent`](#--malt_top_percent)
-      - [`--malt_min_support_mode`](#--malt_min_support_mode)
-      - [`--malt_min_support_percent`](#--malt_min_support_percent)
-      - [`--malt_max_queries`](#--malt_max_queries)
-      - [`--malt_memory_mode`](#--malt_memory_mode)
-      - [`--run_maltextract`](#--run_maltextract)
-      - [`--maltextract_taxon_list`](#--maltextract_taxon_list)
-      - [`--maltextract_ncbifiles`](#--maltextract_ncbifiles)
-      - [`--maltextract_filter`](#--maltextract_filter)
-      - [`--maltextract_toppercent`](#--maltextract_toppercent)
-      - [`--maltextract_destackingoff`](#--maltextract_destackingoff)
-      - [`--maltextract_downsamplingoff`](#--maltextract_downsamplingoff)
-      - [`--maltextract_duplicateremovaloff`](#--maltextract_duplicateremovaloff)
-      - [`--maltextract_matches`](#--maltextract_matches)
-      - [`--maltextract_megansummary`](#--maltextract_megansummary)
-      - [`--maltextract_percentidentity`](#--maltextract_percentidentity)
-      - [`maltextract_topalignment`](#maltextract_topalignment)
   - [Clean up](#clean-up)
 
 ## General Nextflow info
@@ -781,19 +628,19 @@ If you want to filter out reads that don't map to a circular chromosome, turn th
 
 ##### `--bt2_alignmode`
 
-The type of read alignment to use. Options are 'local' or 'end-to-end'. Local allows only partial alignment of read, with ends of reads maybe 'soft-clipped', if provides best alignment score. End-to-end requires all nucleotides to align somehow.  Default is 'local', following [Cahill et al (2018)](https://doi.org/10.1093/molbev/msy018) and [(Poullet and Orlando 2020)](https://doi.org/10.3389/fevo.2020.00105).
+The type of read alignment to use. Options are 'local' or 'end-to-end'. Local allows only partial alignment of read, with ends of reads possibly 'soft-clipped' (i.e. remain unaligned/ignored), if the soft-clipped alignment provides best alignment score. End-to-end requires all nucleotides to be align.  Default is 'local', following [Cahill et al (2018)](https://doi.org/10.1093/molbev/msy018) and [(Poullet and Orlando 2020)](https://doi.org/10.3389/fevo.2020.00105).
 
 ##### `--bt2_sensitivity`
 
 The Bowtie2 'preset' to use. Options: 'no-preset' 'very-fast', 'fast', 'sensitive', or 'very-sensitive'. These strings apply to both `--bt2_alignmode` options. See the Bowtie2 [manual](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line) for actual settings. Default is 'sensitive' (following [Poullet and Orlando (2020)](https://doi.org/10.3389/fevo.2020.00105), when running damaged-data _without_ UDG treatment)
 
 ##### `--bt2n`
 
-The number of mismatches allowed in the seed during seed-and-extend procedure of Bowtie2. This will override any values set with `--bt2_sensitivity`. Default: 0.
+The number of mismatches allowed in the seed during seed-and-extend procedure of Bowtie2. This will override any values set with `--bt2_sensitivity`. Can either be 0 or 1. Default: 0 (i.e. use`--bt2_sensitivity` defaults).
 
 ##### `--bt2l`
 
-The length of the seed substring to use during seeding. This will override any values set with `--bt2_sensitivity`. Default: 0.
+The length of the seed substring to use during seeding. This will override any values set with `--bt2_sensitivity`. Default: 0 (i.e. use`--bt2_sensitivity` defaults: [20 for local and 22 for end-to-end](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line).
 
 ##### `-bt2_trim5`
 

main.nf

@@ -305,6 +305,11 @@ if (params.mapper == 'bowtie2' && params.bt2_sensitivity != 'no-preset' && param
     exit 1, "[nf-core/eager] error: invalid bowtie2 sensitivity mode. Options: 'no-preset', 'very-fast', 'fast', 'sensitive', 'very-sensitive'. Options are for both alignmodes You gave: ${params.bt2_sensitivity}"
 }
 
+if (params.bt2n != 0 && params.bt2n != 1) {
+    exit 1, "[nf-core/eager] error: invalid bowtie2 --bt2n (-N) parameter. Options: 0, 1. You gave: ${params.bt2n}"
+
+}
+
 // Index files provided? Then check whether they are correct and complete
 if( params.bwa_index != '' && (params.mapper == 'bwaaln' | params.mapper == 'bwamem')){
     lastPath = params.bwa_index.lastIndexOf(File.separator)