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Bump software versions for viralrecon modules (#1198)

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* Bump software versions for viralrecon modules

* Remove custom params.save_unaligned from bowtie2_align

* Unify samtools modules and error if input and output names are the same

* Fix ALL the tests
This commit is contained in:
Harshil Patel 2022-01-07 17:52:39 +00:00 committed by GitHub
parent c4549c0ecd
commit e751e5040a
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GPG key ID: 4AEE18F83AFDEB23
44 changed files with 151 additions and 114 deletions
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6
modules/bcftools/concat/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.11--h7c999a4_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcfs) tuple val(meta), path(vcfs)

6
modules/bcftools/consensus/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_CONSENSUS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcf), path(tbi), path(fasta) tuple val(meta), path(vcf), path(tbi), path(fasta)

6
modules/bcftools/filter/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_FILTER {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

6
modules/bcftools/index/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

6
modules/bcftools/isec/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_ISEC {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcfs), path(tbis) tuple val(meta), path(vcfs), path(tbis)

6
modules/bcftools/merge/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_MERGE {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcfs), path(tbis) tuple val(meta), path(vcfs), path(tbis)

6
modules/bcftools/mpileup/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_MPILEUP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/bcftools/norm/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_NORM {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

6
modules/bcftools/query/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_QUERY {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcf), path(index) tuple val(meta), path(vcf), path(index)

6
modules/bcftools/reheader/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_REHEADER {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

6
modules/bcftools/stats/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_STATS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcf) tuple val(meta), path(vcf)

6
modules/bcftools/view/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_VIEW {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null) conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' : 'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }" 'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input: input:
tuple val(meta), path(vcf), path(index) tuple val(meta), path(vcf), path(index)

5
modules/bowtie2/align/main.nf
View file

@ -10,6 +10,7 @@ process BOWTIE2_ALIGN {
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
path index path index
val save_unaligned
output: output:
tuple val(meta), path('*.bam'), emit: bam tuple val(meta), path('*.bam'), emit: bam
@ -22,7 +23,7 @@ process BOWTIE2_ALIGN {
def args2 = task.ext.args2 ?: '' def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) { if (meta.single_end) {
def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : '' def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
""" """
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 \\ bowtie2 \\
@ -42,7 +43,7 @@ process BOWTIE2_ALIGN {
END_VERSIONS END_VERSIONS
""" """
} else { } else {
def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : '' def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
""" """
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'` INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 \\ bowtie2 \\

6
modules/fastp/main.nf
View file

@ -2,10 +2,10 @@ process FASTP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null) conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0' : 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
'quay.io/biocontainers/fastp:0.20.1--h8b12597_0' }" 'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

6
modules/minia/main.nf
View file

@ -2,10 +2,10 @@ process MINIA {
tag "$meta.id" tag "$meta.id"
label 'process_high' label 'process_high'
conda (params.enable_conda ? "bioconda::minia=3.2.4" : null) conda (params.enable_conda ? "bioconda::minia=3.2.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0' : 'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' :
'quay.io/biocontainers/minia:3.2.4--he513fc3_0' }" 'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

6
modules/nanoplot/main.nf
View file

@ -2,10 +2,10 @@ process NANOPLOT {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? 'bioconda::nanoplot=1.38.0' : null) conda (params.enable_conda ? 'bioconda::nanoplot=1.39.0' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0' : 'https://depot.galaxyproject.org/singularity/nanoplot:1.39.0--pyhdfd78af_0' :
'quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0' }" 'quay.io/biocontainers/nanoplot:1.39.0--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(ontfile) tuple val(meta), path(ontfile)

6
modules/pangolin/main.nf
View file

@ -2,10 +2,10 @@ process PANGOLIN {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? 'bioconda::pangolin=3.1.11' : null) conda (params.enable_conda ? 'bioconda::pangolin=3.1.17' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pangolin:3.1.11--pyhdfd78af_1' : 'https://depot.galaxyproject.org/singularity/pangolin:3.1.17--pyhdfd78af_0' :
'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1' }" 'quay.io/biocontainers/pangolin:3.1.17--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)

6
modules/picard/collecthsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null) conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/collectmultiplemetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null) conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/collectwgsmetrics/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null) conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam), path(bai)

6
modules/picard/filtersamreads/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null) conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(readlist) tuple val(meta), path(bam), path(readlist)

6
modules/picard/markduplicates/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null) conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/picard/mergesamfiles/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null) conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input: input:
tuple val(meta), path(bams) tuple val(meta), path(bams)

6
modules/picard/sortsam/main.nf
View file

@ -2,10 +2,10 @@ process PICARD_SORTSAM {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null) conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

5
modules/samtools/ampliconclip/main.nf
View file

@ -22,8 +22,9 @@ process SAMTOOLS_AMPLICONCLIP {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : "" def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : "" def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : ""
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
""" """
samtools \\ samtools \\
ampliconclip \\ ampliconclip \\

5
modules/samtools/bam2fq/main.nf
View file

@ -9,11 +9,11 @@ process SAMTOOLS_BAM2FQ {
input: input:
tuple val(meta), path(inputbam) tuple val(meta), path(inputbam)
val(split) val split
output: output:
tuple val(meta), path("*.fq.gz"), emit: reads tuple val(meta), path("*.fq.gz"), emit: reads
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
@ -50,5 +50,4 @@ process SAMTOOLS_BAM2FQ {
END_VERSIONS END_VERSIONS
""" """
} }
} }

3
modules/samtools/depth/main.nf
View file

@ -12,12 +12,11 @@ process SAMTOOLS_DEPTH {
output: output:
tuple val(meta), path("*.tsv"), emit: tsv tuple val(meta), path("*.tsv"), emit: tsv
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
samtools \\ samtools \\
depth \\ depth \\

9
modules/samtools/faidx/main.nf
View file

@ -11,13 +11,16 @@ process SAMTOOLS_FAIDX {
tuple val(meta), path(fasta) tuple val(meta), path(fasta)
output: output:
tuple val(meta), path ("*.fai") , emit: fai tuple val(meta), path ("*.fai"), emit: fai
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
""" """
samtools faidx $fasta samtools \\
faidx \\
$fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

5
modules/samtools/fastq/main.nf
View file

@ -18,13 +18,14 @@ process SAMTOOLS_FASTQ {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz" def endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz"
""" """
samtools fastq \\ samtools \\
fastq \\
$args \\ $args \\
--threads ${task.cpus-1} \\ --threads ${task.cpus-1} \\
$endedness \\ $endedness \\
$bam $bam
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

1
modules/samtools/fixmate/main.nf
View file

@ -18,7 +18,6 @@ process SAMTOOLS_FIXMATE {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
""" """
samtools \\ samtools \\
fixmate \\ fixmate \\

7
modules/samtools/flagstat/main.nf
View file

@ -17,7 +17,12 @@ process SAMTOOLS_FLAGSTAT {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
""" """
samtools flagstat --threads ${task.cpus-1} $bam > ${bam}.flagstat samtools \\
flagstat \\
--threads ${task.cpus-1} \\
$bam \\
> ${bam}.flagstat
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

6
modules/samtools/idxstats/main.nf
View file

@ -17,7 +17,11 @@ process SAMTOOLS_IDXSTATS {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
""" """
samtools idxstats $bam > ${bam}.idxstats samtools \\
idxstats \\
$bam \\
> ${bam}.idxstats
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

6
modules/samtools/index/main.nf
View file

@ -19,7 +19,11 @@ process SAMTOOLS_INDEX {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
""" """
samtools index -@ ${task.cpus-1} $args $input samtools \\
index \\
-@ ${task.cpus-1} \\
$args \\
$input
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

10
modules/samtools/merge/main.nf
View file

@ -12,7 +12,7 @@ process SAMTOOLS_MERGE {
path fasta path fasta
output: output:
tuple val(meta), path("${prefix}.bam"), optional:true, emit: bam tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
@ -22,7 +22,13 @@ process SAMTOOLS_MERGE {
def file_type = input_files[0].getExtension() def file_type = input_files[0].getExtension()
def reference = fasta ? "--reference ${fasta}" : "" def reference = fasta ? "--reference ${fasta}" : ""
""" """
samtools merge --threads ${task.cpus-1} $args ${reference} ${prefix}.${file_type} $input_files samtools \\
merge \\
--threads ${task.cpus-1} \\
$args \\
${reference} \\
${prefix}.${file_type} \\
$input_files
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

1
modules/samtools/sort/main.nf
View file

@ -17,6 +17,7 @@ process SAMTOOLS_SORT {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
""" """
samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

7
modules/samtools/stats/main.nf
View file

@ -19,7 +19,12 @@ process SAMTOOLS_STATS {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def reference = fasta ? "--reference ${fasta}" : "" def reference = fasta ? "--reference ${fasta}" : ""
""" """
samtools stats --threads ${task.cpus-1} ${reference} ${input} > ${input}.stats samtools \\
stats \\
--threads ${task.cpus-1} \\
${reference} \\
${input} \\
> ${input}.stats
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

9
modules/samtools/view/main.nf
View file

@ -21,8 +21,15 @@ process SAMTOOLS_VIEW {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--reference ${fasta} -C" : "" def reference = fasta ? "--reference ${fasta} -C" : ""
def file_type = input.getExtension() def file_type = input.getExtension()
if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
""" """
samtools view --threads ${task.cpus-1} ${reference} $args $input > ${prefix}.${file_type} samtools \\
view \\
--threads ${task.cpus-1} \\
${reference} \\
$args \\
$input \\
> ${prefix}.${file_type}
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

2
tests/modules/bcftools/concat/test.yml
View file

@ -5,4 +5,4 @@
- bcftools - bcftools
files: files:
- path: output/bcftools/test3.vcf.gz - path: output/bcftools/test3.vcf.gz
md5sum: c400c7458524d889e0967b06ed72534f md5sum: 35c88bfaad20101062e98beb217d7137

6
tests/modules/bcftools/mpileup/test.yml
View file

@ -5,8 +5,8 @@
- bcftools - bcftools
files: files:
- path: output/bcftools/test.bcftools_stats.txt - path: output/bcftools/test.bcftools_stats.txt
md5sum: 74863ef525eef8d87e3119146d281bcf md5sum: 72c506e633413c6b439f95336933984e
- path: output/bcftools/test.vcf.gz.tbi - path: output/bcftools/test.vcf.gz.tbi
md5sum: 0772419c5d819b4caa4aebfcad010c6e md5sum: ae0f17dcc2cb27034d848699b824c516
- path: output/bcftools/test.vcf.gz - path: output/bcftools/test.vcf.gz
md5sum: 9811674bb8da7ff30581319a910f2396 md5sum: e9e520663875c66296f3bff0fa226c40

2
tests/modules/bcftools/stats/test.yml
View file

@ -5,4 +5,4 @@
- bcftools/stats - bcftools/stats
files: files:
- path: output/bcftools/test.bcftools_stats.txt - path: output/bcftools/test.bcftools_stats.txt
md5sum: d3543531396cf7012f13ebdce639cbc8 md5sum: 1f948177196b09806782e1ee801463a2

6
tests/modules/bowtie2/align/main.nf
View file

@ -13,9 +13,10 @@ workflow test_bowtie2_align_single_end {
] ]
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
save_unaligned = false
BOWTIE2_BUILD ( fasta ) BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
} }
workflow test_bowtie2_align_paired_end { workflow test_bowtie2_align_paired_end {
@ -27,7 +28,8 @@ workflow test_bowtie2_align_paired_end {
] ]
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
save_unaligned = false
BOWTIE2_BUILD ( fasta ) BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index ) BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
} }

28
tests/modules/fastp/test.yml
View file

@ -12,9 +12,9 @@
- "Q20 bases: 12922(92.9841%)" - "Q20 bases: 12922(92.9841%)"
- "reads passed filter: 99" - "reads passed filter: 99"
- path: output/fastp/test.trim.fastq.gz - path: output/fastp/test.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test.fastp.json - path: output/fastp/test.fastp.json
md5sum: e0d856ebb3da9e4462c3ce9683efe01d md5sum: a517ba37b17a342b5428f2c1f8fe3dd7
- name: fastp test_fastp_paired_end - name: fastp test_fastp_paired_end
command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@ -33,9 +33,9 @@
contains: contains:
- '"passed_filter_reads": 198' - '"passed_filter_reads": 198'
- path: output/fastp/test_1.trim.fastq.gz - path: output/fastp/test_1.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test_2.trim.fastq.gz - path: output/fastp/test_2.trim.fastq.gz
md5sum: 9eff7203596580cc5e42aceab4a469df md5sum: 532b190fb4dc7b2277ee5cf1464e598c
- name: fastp test_fastp_single_end_trim_fail - name: fastp test_fastp_single_end_trim_fail
command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@ -51,11 +51,11 @@
- "Q20 bases: 12922(92.9841%)" - "Q20 bases: 12922(92.9841%)"
- "reads passed filter: 99" - "reads passed filter: 99"
- path: output/fastp/test.trim.fastq.gz - path: output/fastp/test.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test.fastp.json - path: output/fastp/test.fastp.json
md5sum: ee65a46d6e59fa556f112727b8a902ce md5sum: 4be682c727942a45fc4c8600c28694a8
- path: output/fastp/test.fail.fastq.gz - path: output/fastp/test.fail.fastq.gz
md5sum: de315d397c994d8e66bafc7a8dc11070 md5sum: b57f2026eb259a0b0c0b3960c270258d
- name: fastp test_fastp_paired_end_trim_fail - name: fastp test_fastp_paired_end_trim_fail
command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@ -74,13 +74,13 @@
contains: contains:
- '"passed_filter_reads": 198' - '"passed_filter_reads": 198'
- path: output/fastp/test_1.trim.fastq.gz - path: output/fastp/test_1.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
- path: output/fastp/test_2.trim.fastq.gz - path: output/fastp/test_2.trim.fastq.gz
md5sum: 9eff7203596580cc5e42aceab4a469df md5sum: 532b190fb4dc7b2277ee5cf1464e598c
- path: output/fastp/test_1.fail.fastq.gz - path: output/fastp/test_1.fail.fastq.gz
md5sum: e62ff0123a74adfc6903d59a449cbdb0 md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/fastp/test_2.fail.fastq.gz - path: output/fastp/test_2.fail.fastq.gz
md5sum: f52309b35a7c15cbd56a9c3906ef98a5 md5sum: 72d0002841967676ac936d08746a9128
- name: fastp test_fastp_paired_end_merged - name: fastp test_fastp_paired_end_merged
command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@ -101,8 +101,8 @@
- "total reads: 75" - "total reads: 75"
- "total bases: 13683" - "total bases: 13683"
- path: output/fastp/test.merged.fastq.gz - path: output/fastp/test.merged.fastq.gz
md5sum: ce88539076ced5aff11f866836ea1f40 md5sum: 4955ca2c899729b17bd526d2626a8d73
- path: output/fastp/test_1.trim.fastq.gz - path: output/fastp/test_1.trim.fastq.gz
md5sum: 65d75c13abbfbfd993914e1379634100 md5sum: 4a03721ee252b7c6e81e007550e6ab63
- path: output/fastp/test_2.trim.fastq.gz - path: output/fastp/test_2.trim.fastq.gz
md5sum: 0d87ce4d8ef29fb35f337eb0f6c9fcb4 md5sum: 7a4ddf8485c147cd7aaf0d4f6cd57ace

2
tests/modules/pangolin/test.yml
View file

@ -4,4 +4,4 @@
- pangolin - pangolin
files: files:
- path: ./output/pangolin/test.pangolin.csv - path: ./output/pangolin/test.pangolin.csv
md5sum: 4eaff46b5b11cd59fb44d4e8e7c4945e md5sum: 2563856ee31ba2a4a05705ff940a28cc

2
tests/modules/samtools/stats/test.yml
View file

@ -14,4 +14,4 @@
- samtools - samtools
files: files:
- path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
md5sum: 62377b29c3f6253e37308a28d13a496d md5sum: ab49e7380714b7033e374ba1114e5e54