chore: force update all modules

modules/nf-core/cat/fastq/main.nf

@@ -1,6 +1,6 @@
 process CAT_FASTQ {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -20,9 +20,9 @@ process CAT_FASTQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
-        if (readList.size > 1) {
+        if (readList.size >= 1) {
             """
             cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
 
@@ -33,7 +33,7 @@ process CAT_FASTQ {
             """
         }
     } else {
-        if (readList.size > 2) {
+        if (readList.size >= 2) {
             def read1 = []
             def read2 = []
             readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
@@ -51,7 +51,7 @@ process CAT_FASTQ {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
         if (readList.size > 1) {
             """

modules/nf-core/centrifuge/kreport/main.nf

@@ -1,6 +1,6 @@
 process CENTRIFUGE_KREPORT {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py

@@ -58,11 +58,12 @@ versions_by_module = {}
 for process, process_versions in versions_by_process.items():
     module = process.split(":")[-1]
     try:
-        assert versions_by_module[module] == process_versions, (
+        if versions_by_module[module] != process_versions:
-            "We assume that software versions are the same between all modules. "
+            raise AssertionError(
-            "If you see this error-message it means you discovered an edge-case "
+                "We assume that software versions are the same between all modules. "
-            "and should open an issue in nf-core/tools. "
+                "If you see this error-message it means you discovered an edge-case "
-        )
+                "and should open an issue in nf-core/tools. "
+            )
     except KeyError:
         versions_by_module[module] = process_versions
 

modules/nf-core/eido/convert/main.nf

@@ -1,5 +1,5 @@
 process EIDO_CONVERT {
-    tag '$samplesheet'
+    tag "$samplesheet"
     label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)

modules/nf-core/eido/validate/main.nf

@@ -1,5 +1,5 @@
 process EIDO_VALIDATE {
-    tag '$samplesheet'
+    tag "$samplesheet"
     label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)

modules/nf-core/gunzip/main.nf

@@ -1,6 +1,6 @@
 process GUNZIP {
     tag "$archive"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/kaiju/kaiju2krona/main.nf

@@ -1,6 +1,6 @@
 process KAIJU_KAIJU2KRONA {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/kaiju/kaiju2table/main.nf

@@ -1,6 +1,6 @@
 process KAIJU_KAIJU2TABLE {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/krakentools/combinekreports/main.nf

@@ -1,5 +1,5 @@
 process KRAKENTOOLS_COMBINEKREPORTS {
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/krakentools/kreport2krona/main.nf

@@ -1,6 +1,6 @@
 process KRAKENTOOLS_KREPORT2KRONA {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)

modules/nf-core/krona/ktimporttaxonomy/main.nf

@@ -1,6 +1,6 @@
 process KRONA_KTIMPORTTAXONOMY {
     tag "${meta.id}"
-    label 'process_high'
+    label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::krona=2.8" : null)

modules/nf-core/krona/ktimporttext/main.nf

@@ -1,6 +1,6 @@
 process KRONA_KTIMPORTTEXT {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/megan/rma2info/main.nf

@@ -1,6 +1,6 @@
 process MEGAN_RMA2INFO {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/minimap2/index/main.nf

@@ -7,11 +7,11 @@ process MINIMAP2_INDEX {
         'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
 
     input:
-    path fasta
+    tuple val(meta), path(fasta)
 
     output:
-    path "*.mmi"        , emit: index
+    tuple val(meta), path("*.mmi"), emit: index
-    path "versions.yml" , emit: versions
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/minimap2/index/meta.yml

@@ -12,11 +12,21 @@ tools:
       documentation: https://github.com/lh3/minimap2#uguide
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: |
         Reference database in FASTA format.
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - mmi:
       type: file
       description: Minimap2 fasta index.

modules/nf-core/motus/merge/main.nf

@@ -2,7 +2,7 @@ VERSION = '3.0.1'
 
 process MOTUS_MERGE {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/nf-core/samtools/view/main.nf

@@ -10,31 +10,39 @@ process SAMTOOLS_VIEW {
     input:
     tuple val(meta), path(input), path(index)
     path fasta
+    path qname
 
     output:
-    tuple val(meta), path("*.bam") , emit: bam , optional: true
+    tuple val(meta), path("*.bam"),  emit: bam,     optional: true
-    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    tuple val(meta), path("*.cram"), emit: cram,    optional: true
-    path  "versions.yml"           , emit: versions
+    tuple val(meta), path("*.sam"),  emit: sam,     optional: true
+    tuple val(meta), path("*.bai"),  emit: bai,     optional: true
+    tuple val(meta), path("*.csi"),  emit: csi,     optional: true
+    tuple val(meta), path("*.crai"), emit: crai,    optional: true
+    path  "versions.yml",            emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "--reference ${fasta} -C" : ""
+    def reference = fasta ? "--reference ${fasta}" : ""
-    def file_type = input.getExtension()
+    def readnames = qname ? "--qname-file ${qname}": ""
+    def file_type = args.contains("--output-fmt sam") ? "sam" :
+                    args.contains("--output-fmt bam") ? "bam" :
+                    args.contains("--output-fmt cram") ? "cram" :
+                    input.getExtension()
     if ("$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} \\
+        ${readnames} \\
         $args \\
-        $input \\
+        -o ${prefix}.${file_type} \\
-        $args2 \\
+        $input
-        > ${prefix}.${file_type}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/samtools/view/meta.yml

@@ -33,6 +33,10 @@ input:
       type: optional file
       description: Reference file the CRAM was created with
       pattern: "*.{fasta,fa}"
+  - qname:
+      type: file
+      description: Optional file with read names to output only select alignments
+      pattern: "*.{txt,list}"
 output:
   - meta:
       type: map
@@ -41,12 +45,29 @@ output:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: filtered/converted BAM/SAM file
+      description: optional filtered/converted BAM file
-      pattern: "*.{bam,sam}"
+      pattern: "*.{bam}"
   - cram:
       type: file
-      description: filtered/converted CRAM file
+      description: optional filtered/converted CRAM file
-      pattern: "*.cram"
+      pattern: "*.{cram}"
+  - sam:
+      type: file
+      description: optional filtered/converted SAM file
+      pattern: "*.{sam}"
+  # bai, csi, and crai are created with `--write-index`
+  - bai:
+      type: file
+      description: optional BAM file index
+      pattern: "*.{bai}"
+  - csi:
+      type: file
+      description: optional tabix BAM file index
+      pattern: "*.{csi}"
+  - crai:
+      type: file
+      description: optional CRAM file index
+      pattern: "*.{crai}"
   - versions:
       type: file
       description: File containing software versions
@@ -55,3 +76,4 @@ authors:
   - "@drpatelh"
   - "@joseespinosa"
   - "@FriederikeHanssen"
+  - "@priyanka-surana"

modules/nf-core/untar/main.nf

@@ -27,7 +27,7 @@ process UNTAR {
 
     ## Ensures --strip-components only applied when top level of tar contents is a directory
     ## If just files or multiple directories, place all in output
-    if [[ \$(tar -tzf ${archive} | grep "/\$" | wc -l) -eq 1 ]]; then
+    if [[ \$(tar -tzf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
         tar \\
             -C output --strip-components 1 \\
             -xzvf \\