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Merged
maxulysse merged 6 commits into from
Jul 16, 2020
Merged

Works with Nextflow.20.06.0 edge and has optional processes #244

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4bfc0f9
remove headers from help message
maxulysse Jul 16, 2020
b43b580
fix out issue with nextflow 20.06.0-edge
maxulysse Jul 16, 2020
bb39d07
commit all current changes
maxulysse Jul 16, 2020
ad51434
optional output
maxulysse Jul 16, 2020
bbd462b
trim_galore is optional too
maxulysse Jul 16, 2020
d492db4
use intervals
maxulysse Jul 16, 2020
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43 changes: 21 additions & 22 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,14 @@ nf-core/sarek:

nextflow.preview.dsl = 2

// Print help message if required

if (params.help) {
def command = "nextflow run nf-core/sarek -profile docker --input sample.tsv"
log.info Schema.params_help("$baseDir/nextflow_schema.json", command)
exit 0
}

/*
================================================================================
INCLUDE SAREK FUNCTIONS
Expand Down Expand Up @@ -244,16 +252,6 @@ workflow_summary = Channel.value(workflow_summary)
if ('mutect2' in tools && !(params.pon)) log.warn "[nf-core/sarek] Mutect2 was requested, but as no panel of normals were given, results will not be optimal"
if (params.sentieon) log.warn "[nf-core/sarek] Sentieon will be used, only works if Sentieon is available where nf-core/sarek is run"

// Print help message if required

if (params.help) {
def command = "nextflow run nf-core/sarek --input sample.tsv -profile docker"
log.info Headers.nf_core(workflow, params.monochrome_logs)
log.info Schema.params_help("$baseDir/nextflow_schema.json", command)
exit 0
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@FriederikeHanssen FriederikeHanssen Jul 16, 2020

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Why is this removed?

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@maxulysse maxulysse Jul 16, 2020

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Moved it back to the top, and just removed the Headers part from it, I think it's useless in the help context

}


/*
================================================================================
INCLUDE LOCAL PIPELINE MODULES
Expand Down Expand Up @@ -336,15 +334,14 @@ workflow {
pon,
step)

bwa = params.bwa ? Channel.value(file(params.bwa)) : BUILD_INDICES.out.bwa_built
dict = params.dict ? Channel.value(file(params.dict)) : BUILD_INDICES.out.dictBuilt
fai = params.fasta_fai ? Channel.value(file(params.fasta_fai)) : BUILD_INDICES.out.fai_built
dbsnp_tbi = params.dbsnp ? params.dbsnp_index ? Channel.value(file(params.dbsnp_index)) : BUILD_INDICES.out.dbsnp_tbi : "null"
germline_resource_tbi = params.germline_resource ? params.germline_resource_index ? Channel.value(file(params.germline_resource_index)) : BUILD_INDICES.out.germline_resource_tbi : "null"
known_indels_tbi = params.known_indels ? params.known_indels_index ? Channel.value(file(params.known_indels_index)) : BUILD_INDICES.out.known_indels_tbi.collect() : "null"
pon_tbi = params.pon ? params.pon_index ? Channel.value(file(params.pon_index)) : BUILD_INDICES.out.pon_tbi : "null"
intervals = params.no_intervals ? "null" : params.intervals && !('annotate' in step) ? Channel.value(file(params.intervals)) : BUILD_INDICES.out.intervalBuilt
intervals.dump(tag: 'intervals')
bwa = params.bwa ?: BUILD_INDICES.out.bwa
dbsnp_tbi = params.dbsnp ? params.dbsnp_index ?: BUILD_INDICES.out.dbsnp_tbi : Channel.empty()
dict = params.dict ?: BUILD_INDICES.out.dict
fai = params.fasta_fai ? params.fasta_fai : BUILD_INDICES.out.fai
germline_resource_tbi = params.germline_resource ? params.germline_resource_index ?: BUILD_INDICES.out.germline_resource_tbi : Channel.empty()
intervals = params.no_intervals ? Channel.empty() : params.intervals && !('annotate' in step) ? params.intervals : BUILD_INDICES.out.intervals
known_indels_tbi = params.known_indels ? params.known_indels_index ?: BUILD_INDICES.out.known_indels_tbi.collect() : Channel.empty()
pon_tbi = params.pon ? params.pon_index ?: BUILD_INDICES.out.pon_tbi : Channel.empty()

// PREPROCESSING
if((!params.no_intervals) && step != 'annotate')
Expand Down Expand Up @@ -375,14 +372,16 @@ workflow {
ch_bed_intervals = Channel.from(file("${params.outdir}/no_intervals.bed"))
}

//if(!('fastqc' in skipQC))
// if(!('fastqc' in skipQC))
FASTQC(input_sample)

if(params.trim_fastq) {
if (params.trim_fastq) {
TRIM_GALORE(input_sample)
result_trim_galore = TRIM_GALORE.out.report
BWAMEM2_MEM(TRIM_GALORE.out.trimmed_reads, bwa, fasta, fai)
}
else {
result_trim_galore = Channel.empty()
BWAMEM2_MEM(input_sample, bwa, fasta, fai)
}

Expand All @@ -397,7 +396,7 @@ workflow {
multiqc_config,
multiqc_custom_config.ifEmpty([]),
GET_SOFTWARE_VERSIONS.out.yml,
TRIM_GALORE.out.report.ifEmpty([]),
result_trim_galore.ifEmpty([]),
workflow_summary)
}

Expand Down
2 changes: 0 additions & 2 deletions modules/nf-core/samtools_faidx.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,6 @@ process SAMTOOLS_FAIDX {
output:
path "${fasta}.fai"

//when: !(params.fasta_fai) && params.fasta && !('annotate' in step)

script:
"""
samtools faidx ${fasta}
Expand Down
73 changes: 44 additions & 29 deletions modules/subworkflows/build_indices.nf
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Expand Up @@ -7,59 +7,74 @@
// And then initialize channels based on params or indexes that were just built

include { BUILD_INTERVALS } from '../local/build_intervals.nf'
include { BWAMEM2_INDEX as BWAMEM2_INDEX } from '../nf-core/bwamem2_index.nf'
include { GATK_CREATE_SEQUENCE_DICTIONARY as GATK_CREATE_SEQUENCE_DICTIONARY } from '../local/gatk_dict.nf'
include { BWAMEM2_INDEX } from '../nf-core/bwamem2_index.nf'
include { GATK_CREATE_SEQUENCE_DICTIONARY } from '../local/gatk_dict.nf'
include {
HTSLIB_TABIX as HTSLIB_TABIX_DBSNP;
HTSLIB_TABIX as HTSLIB_TABIX_GERMLINE_RESOURCE;
HTSLIB_TABIX as HTSLIB_TABIX_KNOWN_INDELS;
HTSLIB_TABIX as HTSLIB_TABIX_PON;
} from '../nf-core/htslib_tabix'
include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX } from '../nf-core/samtools_faidx.nf'
include { SAMTOOLS_FAIDX } from '../nf-core/samtools_faidx.nf'

workflow BUILD_INDICES{
take:
ch_dbsnp
ch_fasta
ch_germline_resource
ch_known_indels
ch_pon
dbsnp
fasta
germline_resource
known_indels
pon
step

main:

if (!(params.bwa) && params.fasta && 'mapping' in step)
BWAMEM2_INDEX(ch_fasta)
if (!(params.bwa) && params.fasta && 'mapping' in step)
result_bwa = BWAMEM2_INDEX(fasta)
else
result_bwa = Channel.empty()
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@FriederikeHanssen FriederikeHanssen Jul 16, 2020

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Glad it works like this, but unhappy with the optics

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@maxulysse maxulysse Jul 16, 2020

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We'll improve it at some point


if (!(params.dict) && params.fasta && !('annotate' in step) && !('controlfreec' in step))
GATK_CREATE_SEQUENCE_DICTIONARY(ch_fasta)
result_dict = GATK_CREATE_SEQUENCE_DICTIONARY(fasta)
else
result_dict = Channel.empty()

if (!(params.fasta_fai) && params.fasta && !('annotate' in step))
SAMTOOLS_FAIDX(ch_fasta)
result_fai = SAMTOOLS_FAIDX(fasta)
else
result_fai = Channel.empty()

if (!(params.dbsnp_index) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools || 'mutect2' in tools || 'tnscope' in tools))
HTSLIB_TABIX_DBSNP(ch_dbsnp)

result_dbsnp_tbi = HTSLIB_TABIX_DBSNP(dbsnp)
else
result_dbsnp_tbi = Channel.empty()

if (!(params.germline_resource_index) && params.germline_resource && 'mutect2' in tools)
HTSLIB_TABIX_GERMLINE_RESOURCE(ch_germline_resource)

result_germline_resource_tbi = HTSLIB_TABIX_GERMLINE_RESOURCE(germline_resource)
else
result_germline_resource_tbi = Channel.empty()

if (!(params.known_indels_index) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step))
HTSLIB_TABIX_KNOWN_INDELS(ch_known_indels)
result_known_indels_tbi = HTSLIB_TABIX_KNOWN_INDELS(known_indels)
else
result_known_indels_tbi = Channel.empty()

if (!(params.pon_index) && params.pon && ('tnscope' in tools || 'mutect2' in tools))
HTSLIB_TABIX_PON(ch_pon)
result_pon_tbi = HTSLIB_TABIX_PON(pon)
else
result_pon_tbi = Channel.empty()

if (!(params.intervals) && !('annotate' in step) && !('controlfreec' in step)) {
BUILD_INTERVALS(SAMTOOLS_FAIDX.out)
}
if (!(params.intervals) && !('annotate' in step) && !('controlfreec' in step))
result_intervals = BUILD_INTERVALS(SAMTOOLS_FAIDX.out)
else
result_intervals = Channel.empty()

emit:
bwa_built = BWAMEM2_INDEX.out
dbsnp_tbi = HTSLIB_TABIX_DBSNP.out
dictBuilt = GATK_CREATE_SEQUENCE_DICTIONARY.out
fai_built = SAMTOOLS_FAIDX.out
germline_resource_tbi = HTSLIB_TABIX_GERMLINE_RESOURCE.out
intervalBuilt = BUILD_INTERVALS.out
known_indels_tbi = HTSLIB_TABIX_KNOWN_INDELS.out
pon_tbi = HTSLIB_TABIX_PON.out
bwa = result_bwa
dbsnp_tbi = result_dbsnp_tbi
dict = result_dict
fai = result_fai
germline_resource_tbi = result_germline_resource_tbi
intervals = result_intervals
known_indels_tbi = result_known_indels_tbi
pon_tbi = result_pon_tbi
}
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