mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Merge branch 'master' into subwf/bam_qc
This commit is contained in:
commit
3997d28a77
22 changed files with 83 additions and 87 deletions
|
@ -27,8 +27,8 @@ process MINIMAP2_ALIGN {
|
|||
def prefix = task.ext.prefix ?: "${meta.id}"
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||||
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
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def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
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def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
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def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
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def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
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def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
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"""
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minimap2 \\
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$args \\
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||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
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tag "$meta.id"
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label 'process_low'
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||||
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||||
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
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conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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||||
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
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||||
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input:
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tuple val(meta), path(bam)
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@ -38,12 +38,12 @@ process PICARD_ADDORREPLACEREADGROUPS {
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-Xmx${avail_mem}g \\
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--INPUT ${bam} \\
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--OUTPUT ${prefix}.bam \\
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-ID ${ID} \\
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-LB ${LIBRARY} \\
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-PL ${PLATFORM} \\
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-PU ${BARCODE} \\
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-SM ${SAMPLE} \\
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-CREATE_INDEX true
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--RGID ${ID} \\
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--RGLB ${LIBRARY} \\
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--RGPL ${PLATFORM} \\
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--RGPU ${BARCODE} \\
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--RGSM ${SAMPLE} \\
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--CREATE_INDEX true
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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|
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@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
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||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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||||
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
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||||
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input:
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||||
tuple val(meta), path(bam)
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@ -31,8 +31,8 @@ process PICARD_CLEANSAM {
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-Xmx${avail_mem}g \\
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CleanSam \\
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${args} \\
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-I ${bam} \\
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-O ${prefix}.bam
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--INPUT ${bam} \\
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--OUTPUT ${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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|
|
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@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
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tag "$meta.id"
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label 'process_medium'
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||||
|
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conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
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||||
|
||||
input:
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||||
tuple val(meta), path(bam)
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||||
|
@ -38,10 +38,10 @@ process PICARD_COLLECTHSMETRICS {
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CollectHsMetrics \\
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$args \\
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$reference \\
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-BAIT_INTERVALS $bait_intervals \\
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-TARGET_INTERVALS $target_intervals \\
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-INPUT $bam \\
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-OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
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--BAIT_INTERVALS $bait_intervals \\
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--TARGET_INTERVALS $target_intervals \\
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--INPUT $bam \\
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--OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
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||||
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||||
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||||
cat <<-END_VERSIONS > versions.yml
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||||
|
|
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@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
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tag "$meta.id"
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label 'process_medium'
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||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
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||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
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|
@ -33,9 +33,9 @@ process PICARD_COLLECTMULTIPLEMETRICS {
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-Xmx${avail_mem}g \\
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CollectMultipleMetrics \\
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$args \\
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INPUT=$bam \\
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OUTPUT=${prefix}.CollectMultipleMetrics \\
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REFERENCE_SEQUENCE=$fasta
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--INPUT $bam \\
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--OUTPUT ${prefix}.CollectMultipleMetrics \\
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--REFERENCE_SEQUENCE $fasta
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||||
cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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||||
|
|
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@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
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tag "$meta.id"
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label 'process_medium'
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||||
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||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
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||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
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tuple val(meta), path(bam)
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path fasta
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||||
|
||||
output:
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||||
|
@ -32,9 +32,10 @@ process PICARD_COLLECTWGSMETRICS {
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|||
-Xmx${avail_mem}g \\
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CollectWgsMetrics \\
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$args \\
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INPUT=$bam \\
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OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
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REFERENCE_SEQUENCE=$fasta
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--INPUT $bam \\
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--OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
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||||
--REFERENCE_SEQUENCE $fasta
|
||||
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
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|||
tag "$meta.id"
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||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
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|||
-Xmx${avail_mem}g \\
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||||
CreateSequenceDictionary \\
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||||
$args \\
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||||
R=$fasta \\
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||||
O=${prefix}.dict
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||||
--REFERENCE $fasta \\
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||||
--OUTPUT ${prefix}.dict
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
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|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input1)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(readlist)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
@ -31,8 +31,8 @@ process PICARD_FIXMATEINFORMATION {
|
|||
picard \\
|
||||
FixMateInformation \\
|
||||
-Xmx${avail_mem}g \\
|
||||
-I ${bam} \\
|
||||
-O ${prefix}.bam \\
|
||||
--INPUT ${bam} \\
|
||||
--OUTPUT ${prefix}.bam \\
|
||||
--VALIDATION_STRINGENCY ${STRINGENCY}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input_vcf)
|
||||
|
@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
|
|||
-Xmx${avail_mem}g \\
|
||||
LiftoverVcf \\
|
||||
$args \\
|
||||
I=$input_vcf \\
|
||||
O=${prefix}.lifted.vcf.gz \\
|
||||
CHAIN=$chain \\
|
||||
REJECT=${prefix}.unlifted.vcf.gz \\
|
||||
R=$fasta
|
||||
--INPUT $input_vcf \\
|
||||
--OUTPUT ${prefix}.lifted.vcf.gz \\
|
||||
--CHAIN $chain \\
|
||||
--REJECT ${prefix}.unlifted.vcf.gz \\
|
||||
--REFERENCE_SEQUENCE $fasta
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
|
|||
-Xmx${avail_mem}g \\
|
||||
MarkDuplicates \\
|
||||
$args \\
|
||||
I=$bam \\
|
||||
O=${prefix}.bam \\
|
||||
M=${prefix}.MarkDuplicates.metrics.txt
|
||||
--INPUT $bam \\
|
||||
--OUTPUT ${prefix}.bam \\
|
||||
--METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams)
|
||||
|
@ -33,8 +33,8 @@ process PICARD_MERGESAMFILES {
|
|||
-Xmx${avail_mem}g \\
|
||||
MergeSamFiles \\
|
||||
$args \\
|
||||
${'INPUT='+bam_files.join(' INPUT=')} \\
|
||||
OUTPUT=${prefix}.bam
|
||||
${'--INPUT '+bam_files.join(' --INPUT ')} \\
|
||||
--OUTPUT ${prefix}.bam
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_SORTSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_SORTVCF {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
@ -22,8 +22,8 @@ process PICARD_SORTVCF {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
|
||||
def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
|
||||
def seq_dict = sequence_dict ? "--SEQUENCE_DICTIONARY $sequence_dict" : ""
|
||||
def reference = reference ? "--REFERENCE_SEQUENCE $reference" : ""
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
|
|
|
@ -7,4 +7,3 @@
|
|||
- path: output/picard/test.bam
|
||||
md5sum: 7b82f3461c2d80fc6a10385e78c9427f
|
||||
- path: output/picard/versions.yml
|
||||
md5sum: 8a2d176295e1343146ea433c79bb517f
|
||||
|
|
|
@ -7,4 +7,3 @@
|
|||
- path: output/picard/test.bam
|
||||
md5sum: a48f8e77a1480445efc57570c3a38a68
|
||||
- path: output/picard/versions.yml
|
||||
md5sum: e6457d7c6de51bf6f4b577eda65e57ac
|
||||
|
|
|
@ -6,8 +6,7 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
|
|||
|
||||
workflow test_picard_collectwgsmetrics {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||||
]
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
|
||||
|
|
|
@ -7,4 +7,3 @@
|
|||
- path: output/picard/test.dict
|
||||
contains: ["SN:MT192765.1"]
|
||||
- path: output/picard/versions.yml
|
||||
md5sum: b3d8c7ea65b8a6d3237b153d13fe2014
|
||||
|
|
|
@ -7,4 +7,3 @@
|
|||
- path: output/picard/test.bam
|
||||
md5sum: 746102e8c242c0ef42e045c49d320030
|
||||
- path: output/picard/versions.yml
|
||||
md5sum: 4329ba7cdca8f4f6018dfd5c019ba2eb
|
||||
|
|
|
@ -1,5 +1,5 @@
|
|||
process {
|
||||
ext.args = "WARN_ON_MISSING_CONTIG=true"
|
||||
ext.args = "--WARN_ON_MISSING_CONTIG true"
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
|
|
|
@ -3,7 +3,7 @@ process {
|
|||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName: PICARD_MARKDUPLICATES_UNSORTED {
|
||||
ext.args = 'ASSUME_SORT_ORDER=queryname'
|
||||
ext.args = '--ASSUME_SORT_ORDER queryname'
|
||||
}
|
||||
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue