Bump software versions for viralrecon modules (#1198)

* 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
2024-12-22 02:58:17 +00:00 · 2022-01-07 17:52:39 +00:00 · 2022-01-07 17:52:39 +00:00 · e751e5040a
commit e751e5040a
parent c4549c0ecd
44 changed files with 151 additions and 114 deletions
--- a/modules/bcftools/concat/main.nf
+++ b/modules/bcftools/concat/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0' :
-        'quay.io/biocontainers/bcftools:1.11--h7c999a4_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcfs)
--- a/modules/bcftools/consensus/main.nf
+++ b/modules/bcftools/consensus/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_CONSENSUS {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf), path(tbi), path(fasta)
--- a/modules/bcftools/filter/main.nf
+++ b/modules/bcftools/filter/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_FILTER {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf)
--- a/modules/bcftools/index/main.nf
+++ b/modules/bcftools/index/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf)
--- a/modules/bcftools/isec/main.nf
+++ b/modules/bcftools/isec/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_ISEC {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcfs), path(tbis)
--- a/modules/bcftools/merge/main.nf
+++ b/modules/bcftools/merge/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_MERGE {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcfs), path(tbis)
--- a/modules/bcftools/mpileup/main.nf
+++ b/modules/bcftools/mpileup/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_MPILEUP {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/bcftools/norm/main.nf
+++ b/modules/bcftools/norm/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_NORM {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf)
--- a/modules/bcftools/query/main.nf
+++ b/modules/bcftools/query/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_QUERY {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf), path(index)
--- a/modules/bcftools/reheader/main.nf
+++ b/modules/bcftools/reheader/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_REHEADER {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf)
--- a/modules/bcftools/stats/main.nf
+++ b/modules/bcftools/stats/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_STATS {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf)
--- a/modules/bcftools/view/main.nf
+++ b/modules/bcftools/view/main.nf
@ -2,10 +2,10 @@ process BCFTOOLS_VIEW {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"

    input:
    tuple val(meta), path(vcf), path(index)
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@ -10,6 +10,7 @@ process BOWTIE2_ALIGN {
    input:
    tuple val(meta), path(reads)
    path  index
+    val   save_unaligned

    output:
    tuple val(meta), path('*.bam'), emit: bam
@ -22,7 +23,7 @@ process BOWTIE2_ALIGN {
    def args2 = task.ext.args2 ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    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//'`
        bowtie2 \\
@ -42,7 +43,7 @@ process BOWTIE2_ALIGN {
        END_VERSIONS
        """
    } else {
-        def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
+        def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
        """
        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
        bowtie2 \\
--- a/modules/fastp/main.nf
+++ b/modules/fastp/main.nf
@ -2,10 +2,10 @@ process FASTP {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0' :
-        'quay.io/biocontainers/fastp:0.20.1--h8b12597_0' }"
+        'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
+        'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/minia/main.nf
+++ b/modules/minia/main.nf
@ -2,10 +2,10 @@ process MINIA {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0' :
-        'quay.io/biocontainers/minia:3.2.4--he513fc3_0' }"
+        'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' :
+        'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/nanoplot/main.nf
+++ b/modules/nanoplot/main.nf
@ -2,10 +2,10 @@ process NANOPLOT {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0' :
-        'quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/nanoplot:1.39.0--pyhdfd78af_0' :
+        'quay.io/biocontainers/nanoplot:1.39.0--pyhdfd78af_0' }"

    input:
    tuple val(meta), path(ontfile)
--- a/modules/pangolin/main.nf
+++ b/modules/pangolin/main.nf
@ -2,10 +2,10 @@ process PANGOLIN {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/pangolin:3.1.11--pyhdfd78af_1' :
-        'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/pangolin:3.1.17--pyhdfd78af_0' :
+        'quay.io/biocontainers/pangolin:3.1.17--pyhdfd78af_0' }"

    input:
    tuple val(meta), path(fasta)
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam), path(bai)
--- a/modules/picard/filtersamreads/main.nf
+++ b/modules/picard/filtersamreads/main.nf
@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam), path(readlist)
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"

    input:
    tuple val(meta), path(bams)
--- a/modules/picard/sortsam/main.nf
+++ b/modules/picard/sortsam/main.nf
@ -2,10 +2,10 @@ process PICARD_SORTSAM {
    tag "$meta.id"
    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 ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"

    input:
    tuple val(meta), path(bam)
--- a/modules/samtools/ampliconclip/main.nf
+++ b/modules/samtools/ampliconclip/main.nf
@ -22,8 +22,9 @@ process SAMTOOLS_AMPLICONCLIP {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
-    def rejects  = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
-    def stats    = save_clipstats   ? "-f ${prefix}.clipstats.txt"               : ""
+    def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
+    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 \\
        ampliconclip \\
--- a/modules/samtools/bam2fq/main.nf
+++ b/modules/samtools/bam2fq/main.nf
@ -9,11 +9,11 @@ process SAMTOOLS_BAM2FQ {

    input:
    tuple val(meta), path(inputbam)
-    val(split)
+    val split

    output:
    tuple val(meta), path("*.fq.gz"), emit: reads
-    path "versions.yml"          , emit: versions
+    path "versions.yml"             , emit: versions

    script:
    def args = task.ext.args ?: ''
@ -50,5 +50,4 @@ process SAMTOOLS_BAM2FQ {
        END_VERSIONS
        """
    }
-
 }
--- a/modules/samtools/depth/main.nf
+++ b/modules/samtools/depth/main.nf
@ -12,12 +12,11 @@ process SAMTOOLS_DEPTH {

    output:
    tuple val(meta), path("*.tsv"), emit: tsv
-    path "versions.yml"          , emit: versions
+    path "versions.yml"           , emit: versions

    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
-
    """
    samtools \\
        depth \\
--- a/modules/samtools/faidx/main.nf
+++ b/modules/samtools/faidx/main.nf
@ -11,13 +11,16 @@ process SAMTOOLS_FAIDX {
    tuple val(meta), path(fasta)

    output:
-    tuple val(meta), path ("*.fai") , emit: fai
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path ("*.fai"), emit: fai
+    path "versions.yml"            , emit: versions

    script:
    def args = task.ext.args ?: ''
    """
-    samtools faidx $fasta
+    samtools \\
+        faidx \\
+        $fasta
+
    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
--- a/modules/samtools/fastq/main.nf
+++ b/modules/samtools/fastq/main.nf
@ -18,13 +18,14 @@ process SAMTOOLS_FASTQ {
    def args = task.ext.args ?: ''
    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"
-
    """
-    samtools fastq \\
+    samtools \\
+        fastq \\
        $args \\
        --threads ${task.cpus-1} \\
        $endedness \\
        $bam
+
    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
--- a/modules/samtools/fixmate/main.nf
+++ b/modules/samtools/fixmate/main.nf
@ -18,7 +18,6 @@ process SAMTOOLS_FIXMATE {
    def args = task.ext.args ?: ''
    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 \\
        fixmate  \\
--- a/modules/samtools/flagstat/main.nf
+++ b/modules/samtools/flagstat/main.nf
@ -17,7 +17,12 @@ process SAMTOOLS_FLAGSTAT {
    script:
    def args = task.ext.args ?: ''
    """
-    samtools flagstat --threads ${task.cpus-1} $bam > ${bam}.flagstat
+    samtools \\
+        flagstat \\
+        --threads ${task.cpus-1} \\
+        $bam \\
+        > ${bam}.flagstat
+
    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
--- a/modules/samtools/idxstats/main.nf
+++ b/modules/samtools/idxstats/main.nf
@ -17,7 +17,11 @@ process SAMTOOLS_IDXSTATS {
    script:
    def args = task.ext.args ?: ''
    """
-    samtools idxstats $bam > ${bam}.idxstats
+    samtools \\
+        idxstats \\
+        $bam \\
+        > ${bam}.idxstats
+
    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
--- a/modules/samtools/index/main.nf
+++ b/modules/samtools/index/main.nf
@ -19,7 +19,11 @@ process SAMTOOLS_INDEX {
    script:
    def args = task.ext.args ?: ''
    """
-    samtools index -@ ${task.cpus-1} $args $input
+    samtools \\
+        index \\
+        -@ ${task.cpus-1} \\
+        $args \\
+        $input

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
--- a/modules/samtools/merge/main.nf
+++ b/modules/samtools/merge/main.nf
@ -12,7 +12,7 @@ process SAMTOOLS_MERGE {
    path fasta

    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
    path  "versions.yml"                                  , emit: versions

@ -22,7 +22,13 @@ process SAMTOOLS_MERGE {
    def file_type = input_files[0].getExtension()
    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
    "${task.process}":
--- a/modules/samtools/sort/main.nf
+++ b/modules/samtools/sort/main.nf
@ -17,6 +17,7 @@ process SAMTOOLS_SORT {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${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
    cat <<-END_VERSIONS > versions.yml
--- a/modules/samtools/stats/main.nf
+++ b/modules/samtools/stats/main.nf
@ -19,7 +19,12 @@ process SAMTOOLS_STATS {
    def args = task.ext.args ?: ''
    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
    "${task.process}":
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@ -21,8 +21,15 @@ process SAMTOOLS_VIEW {
    def prefix = task.ext.prefix ?: "${meta.id}"
    def reference = fasta ? "--reference ${fasta} -C" : ""
    def file_type = input.getExtension()
+    if ("$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
    "${task.process}":
--- a/tests/modules/bcftools/concat/test.yml
+++ b/tests/modules/bcftools/concat/test.yml
@ -5,4 +5,4 @@
    - bcftools
  files:
    - path: output/bcftools/test3.vcf.gz
-      md5sum: c400c7458524d889e0967b06ed72534f
+      md5sum: 35c88bfaad20101062e98beb217d7137
--- a/tests/modules/bcftools/mpileup/test.yml
+++ b/tests/modules/bcftools/mpileup/test.yml
@ -5,8 +5,8 @@
    - bcftools
  files:
    - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 74863ef525eef8d87e3119146d281bcf
+      md5sum: 72c506e633413c6b439f95336933984e
    - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 0772419c5d819b4caa4aebfcad010c6e
+      md5sum: ae0f17dcc2cb27034d848699b824c516
    - path: output/bcftools/test.vcf.gz
-      md5sum: 9811674bb8da7ff30581319a910f2396
+      md5sum: e9e520663875c66296f3bff0fa226c40
--- a/tests/modules/bcftools/stats/test.yml
+++ b/tests/modules/bcftools/stats/test.yml
@ -5,4 +5,4 @@
    - bcftools/stats
  files:
    - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: d3543531396cf7012f13ebdce639cbc8
+      md5sum: 1f948177196b09806782e1ee801463a2
--- a/tests/modules/bowtie2/align/main.nf
+++ b/tests/modules/bowtie2/align/main.nf
@ -13,9 +13,10 @@ workflow test_bowtie2_align_single_end {
        ]
    ]
    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false

    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 {
@ -27,7 +28,8 @@ workflow test_bowtie2_align_paired_end {
        ]
    ]
    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false

    BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
 }
--- a/tests/modules/fastp/test.yml
+++ b/tests/modules/fastp/test.yml
@ -12,9 +12,9 @@
        - "Q20 bases: 12922(92.9841%)"
        - "reads passed filter: 99"
    - path: output/fastp/test.trim.fastq.gz
-      md5sum: e2257263668dc8a75d95475099fb472d
+      md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
    - path: output/fastp/test.fastp.json
-      md5sum: e0d856ebb3da9e4462c3ce9683efe01d
+      md5sum: a517ba37b17a342b5428f2c1f8fe3dd7

 - 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
@ -33,9 +33,9 @@
      contains:
        - '"passed_filter_reads": 198'
    - path: output/fastp/test_1.trim.fastq.gz
-      md5sum: e2257263668dc8a75d95475099fb472d
+      md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
    - path: output/fastp/test_2.trim.fastq.gz
-      md5sum: 9eff7203596580cc5e42aceab4a469df
+      md5sum: 532b190fb4dc7b2277ee5cf1464e598c

 - 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
@ -51,11 +51,11 @@
        - "Q20 bases: 12922(92.9841%)"
        - "reads passed filter: 99"
    - path: output/fastp/test.trim.fastq.gz
-      md5sum: e2257263668dc8a75d95475099fb472d
+      md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
    - path: output/fastp/test.fastp.json
-      md5sum: ee65a46d6e59fa556f112727b8a902ce
+      md5sum: 4be682c727942a45fc4c8600c28694a8
    - path: output/fastp/test.fail.fastq.gz
-      md5sum: de315d397c994d8e66bafc7a8dc11070
+      md5sum: b57f2026eb259a0b0c0b3960c270258d

 - 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
@ -74,13 +74,13 @@
      contains:
        - '"passed_filter_reads": 198'
    - path: output/fastp/test_1.trim.fastq.gz
-      md5sum: e2257263668dc8a75d95475099fb472d
+      md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
    - path: output/fastp/test_2.trim.fastq.gz
-      md5sum: 9eff7203596580cc5e42aceab4a469df
+      md5sum: 532b190fb4dc7b2277ee5cf1464e598c
    - path: output/fastp/test_1.fail.fastq.gz
-      md5sum: e62ff0123a74adfc6903d59a449cbdb0
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: output/fastp/test_2.fail.fastq.gz
-      md5sum: f52309b35a7c15cbd56a9c3906ef98a5
+      md5sum: 72d0002841967676ac936d08746a9128

 - 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
@ -101,8 +101,8 @@
        - "total reads: 75"
        - "total bases: 13683"
    - path: output/fastp/test.merged.fastq.gz
-      md5sum: ce88539076ced5aff11f866836ea1f40
+      md5sum: 4955ca2c899729b17bd526d2626a8d73
    - path: output/fastp/test_1.trim.fastq.gz
-      md5sum: 65d75c13abbfbfd993914e1379634100
+      md5sum: 4a03721ee252b7c6e81e007550e6ab63
    - path: output/fastp/test_2.trim.fastq.gz
-      md5sum: 0d87ce4d8ef29fb35f337eb0f6c9fcb4
+      md5sum: 7a4ddf8485c147cd7aaf0d4f6cd57ace
--- a/tests/modules/pangolin/test.yml
+++ b/tests/modules/pangolin/test.yml
@ -4,4 +4,4 @@
    - pangolin
  files:
    - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 4eaff46b5b11cd59fb44d4e8e7c4945e
+      md5sum: 2563856ee31ba2a4a05705ff940a28cc
--- a/tests/modules/samtools/stats/test.yml
+++ b/tests/modules/samtools/stats/test.yml
@ -14,4 +14,4 @@
    - samtools
  files:
    - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
-      md5sum: 62377b29c3f6253e37308a28d13a496d
+      md5sum: ab49e7380714b7033e374ba1114e5e54