split untar out

nf-core · Dec 13, 2024 · cb6eedb · cb6eedb
1 parent 49457f3
commit cb6eedb
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Showing 3 changed files with 21 additions and 27 deletions.
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
@@ -2,9 +2,6 @@ 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
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
@@ -1,46 +1,46 @@
 process UNTAR {
-    tag "${archive}"
+    tag "$archive"
     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/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
-        : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
+        'nf-core/ubuntu:22.04' }"
 
     input:
     tuple val(meta), path(archive)
 
     output:
-    tuple val(meta), path("${prefix}"), emit: untar
-    path "versions.yml", emit: versions
+    tuple val(meta), path("$prefix"), emit: untar
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
+    prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
 
     """
-    mkdir ${prefix}
+    mkdir $prefix
 
     ## Ensures --strip-components only applied when top level of tar contents is a directory
     ## If just files or multiple directories, place all in prefix
     if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
         tar \\
-            -C ${prefix} --strip-components 1 \\
+            -C $prefix --strip-components 1 \\
             -xavf \\
-            ${args} \\
-            ${archive} \\
-            ${args2}
+            $args \\
+            $archive \\
+            $args2
     else
         tar \\
-            -C ${prefix} \\
+            -C $prefix \\
             -xavf \\
-            ${args} \\
-            ${archive} \\
-            ${args2}
+            $args \\
+            $archive \\
+            $args2
     fi
 
     cat <<-END_VERSIONS > versions.yml
@@ -50,7 +50,7 @@ process UNTAR {
     """
 
     stub:
-    prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
+    prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
     """
     mkdir ${prefix}
     ## Dry-run untaring the archive to get the files and place all in prefix

diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
@@ -28,12 +28,9 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-          pattern: "*/"
-      - ${prefix}:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+      - $prefix:
+          type: directory
+          description: Directory containing contents of archive
           pattern: "*/"
   - versions:
       - versions.yml: