Replace ubuntu for all modules using it - meta PR

modules/nf-core/cat/fastq/environment.yml

@@ -3,3 +3,8 @@ channels:
   - bioconda
 dependencies:
   - conda-forge::coreutils=9.5
+  - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34

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

@@ -1,26 +1,26 @@
 process CAT_FASTQ {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' :
-        'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
+        : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
 
     output:
     tuple val(meta), path("*.merged.fastq.gz"), emit: reads
-    path "versions.yml"                       , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
+    def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
     if (meta.single_end) {
         if (readList.size >= 1) {
             """
@@ -32,11 +32,12 @@ process CAT_FASTQ {
             END_VERSIONS
             """
         }
-    } else {
+    }
+    else {
         if (readList.size >= 2) {
             def read1 = []
             def read2 = []
-            readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
+            readList.eachWithIndex { v, ix -> (ix & 1 ? read2 : read1) << v }
             """
             cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
             cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
@@ -51,7 +52,7 @@ process CAT_FASTQ {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
+    def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
     if (meta.single_end) {
         if (readList.size >= 1) {
             """
@@ -63,7 +64,8 @@ process CAT_FASTQ {
             END_VERSIONS
             """
         }
-    } else {
+    }
+    else {
         if (readList.size >= 2) {
             """
             echo '' | gzip > ${prefix}_1.merged.fastq.gz

modules/nf-core/custom/tabulartogseacls/environment.yml

@@ -2,4 +2,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::coreutils=8.30
+  - conda-forge::coreutils=9.5
+  - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34

modules/nf-core/custom/tabulartogseacls/main.nf

@@ -1,34 +1,36 @@
 process CUSTOM_TABULARTOGSEACLS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
+        : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
 
     input:
     tuple val(meta), path(samples)
 
     output:
     tuple val(meta), path("*.cls"), emit: cls
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: []
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def separator = args.separator ? "${args.separator}" : ( samples.getName().endsWith(".tsv") ? '\t': ',' )
-    separator = separator == '\t' ? '\\t': separator
+    def separator = args.separator ? "${args.separator}" : (samples.getName().endsWith(".tsv") ? '\t' : ',')
+    separator = separator == '\t' ? '\\t' : separator
     def variable = args.variable
-    if ( !variable ) error "Supply a variable in the sample sheet from which to derive classes"
+    if (!variable) {
+        error("Supply a variable in the sample sheet from which to derive classes")
+    }
     """
     cls_file=${prefix}.cls
 
-    column_number=\$(cat $samples | head -n 1 | tr '$separator' "\\n" | grep -En "^$variable\$" | awk -F':' '{print \$1}')
-    classes=\$(tail -n +2 $samples | awk -F'$separator' '{print \$'\$column_number'}' | sed 's/^\$/empty/g')
+    column_number=\$(cat ${samples} | head -n 1 | tr '${separator}' "\\n" | grep -En "^${variable}\$" | awk -F':' '{print \$1}')
+    classes=\$(tail -n +2 ${samples} | awk -F'${separator}' '{print \$'\$column_number'}' | sed 's/^\$/empty/g')
     unique_classes=\$(echo -e "\$classes" | awk '!x[\$0]++')
 
     echo -e "\$(echo -e \"\$classes\" | wc -l) \$(echo -e \"\$unique_classes\" | wc -l) 1" > \$cls_file

modules/nf-core/custom/tabulartogseagct/environment.yml

@@ -2,4 +2,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::coreutils=8.30
+  - conda-forge::coreutils=9.5
+  - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34

modules/nf-core/custom/tabulartogseagct/main.nf

@@ -1,36 +1,36 @@
 process CUSTOM_TABULARTOGSEAGCT {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
+        : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
 
     input:
     tuple val(meta), path(tabular)
 
     output:
     tuple val(meta), path("*.gct"), emit: gct
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: []
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def separator = args.separator ? "${args.separator}" : ( tabular.getName().endsWith(".csv") ? ',': '\t' )
-    separator = separator == '\t' ? '\\t': separator
+    def separator = args.separator ? "${args.separator}" : (tabular.getName().endsWith(".csv") ? ',' : '\t')
+    separator = separator == '\t' ? '\\t' : separator
 
     """
-    n_columns=\$(head -n 1 $tabular | tr "$separator" "\\n" | wc -l)
-    n_lines=\$(wc -l < $tabular)
+    n_columns=\$(head -n 1 ${tabular} | tr "${separator}" "\\n" | wc -l)
+    n_lines=\$(wc -l < ${tabular})
     gct_file=${prefix}.gct
 
     echo -e "#1.2\$(printf '\\t%.0s' {1..\$n_columns})\\n\$((n_lines-1))\\t\$((n_columns-1))\$(printf '\\t%.0s' {1..\$((n_columns-1))})" > \$gct_file
-    echo -e "NAME\\tDESCRIPTION\\t\$(head -n 1 $tabular | cut -f1 -d\$'$separator' --complement | awk -F'$separator' 'BEGIN { OFS = "\\t"}; {\$1=\$1}1' )" >> \$gct_file
-    cat $tabular | tail -n +2 | awk -F'$separator' 'BEGIN { OFS = "\\t"} {\$1=\$1"\\tNA"}1' >> \$gct_file
+    echo -e "NAME\\tDESCRIPTION\\t\$(head -n 1 ${tabular} | cut -f1 -d\$'${separator}' --complement | awk -F'${separator}' 'BEGIN { OFS = "\\t"}; {\$1=\$1}1' )" >> \$gct_file
+    cat ${tabular} | tail -n +2 | awk -F'${separator}' 'BEGIN { OFS = "\\t"} {\$1=\$1"\\tNA"}1' >> \$gct_file
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/igv/js/environment.yml

@@ -2,6 +2,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - conda-forge::coreutils=9.5
   - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
   - conda-forge::sed=4.8
   - conda-forge::tar=1.34

modules/nf-core/igv/js/main.nf

@@ -1,21 +1,20 @@
-
 process IGV_JS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
-        'nf-core/ubuntu:22.04' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
+        : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
 
     input:
     tuple val(meta), path(alignment), path(index)
 
     output:
-    tuple val(meta), path("*_genome-browser.html") , emit: browser
-    tuple val(meta), path(alignment)               , emit: align_files
-    tuple val(meta), path(index)                   , emit: index_files
-    path "versions.yml"                            , emit: versions
+    tuple val(meta), path("*_genome-browser.html"), emit: browser
+    tuple val(meta), path(alignment), emit: align_files
+    tuple val(meta), path(index), emit: index_files
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -37,13 +36,13 @@ process IGV_JS {
             var igvDiv = document.getElementById("igv-div");
             var options =
             {
-                $browser_args,
+                ${browser_args},
                 tracks: [
                     {
-                        "name": "$prefix",
-                        "url": "$alignment",
-                        "indexURL": "$index",
-                        $track_args
+                        "name": "${prefix}",
+                        "url": "${alignment}",
+                        "indexURL": "${index}",
+                        ${track_args}
                     }
                 ]
             };

modules/nf-core/igv/js/tests/main.nf.test.snap

@@ -30,7 +30,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,5adf8988fa1079ca8921a8103910ce3d"
+                    "versions.yml:md5,25c78c49dc1223ecf93c6fc9bd069cac"
                 ],
                 "align_files": [
                     [
@@ -60,15 +60,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,5adf8988fa1079ca8921a8103910ce3d"
+                    "versions.yml:md5,25c78c49dc1223ecf93c6fc9bd069cac"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-09-02T14:13:20.460734"
+        "timestamp": "2024-12-13T11:48:39.41332795"
     },
     "test-igv-js": {
         "content": [
@@ -101,7 +101,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,5adf8988fa1079ca8921a8103910ce3d"
+                    "versions.yml:md5,25c78c49dc1223ecf93c6fc9bd069cac"
                 ],
                 "align_files": [
                     [
@@ -131,14 +131,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,5adf8988fa1079ca8921a8103910ce3d"
+                    "versions.yml:md5,25c78c49dc1223ecf93c6fc9bd069cac"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-09-02T14:13:15.009833"
+        "timestamp": "2024-12-13T11:48:31.033398759"
     }
 }

modules/nf-core/md5sum/environment.yml

@@ -2,4 +2,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::coreutils=8.30
+  - conda-forge::coreutils=9.5
+  - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
+  - conda-forge::sed=4.8
+  - conda-forge::tar=1.34