From 661cfbe01232325cfbee68f42a1bb54467be677b Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 2 May 2023 13:19:35 +0200
Subject: [PATCH] Update UNTAR module

---
 modules.json                   |  4 ++--
 modules/nf-core/untar/main.nf  | 31 +++++++++++++++----------------
 modules/nf-core/untar/meta.yml |  1 +
 3 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/modules.json b/modules.json
index 5f0b286..5ac3cb0 100644
--- a/modules.json
+++ b/modules.json
@@ -173,7 +173,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
+                        "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
                         "installed_by": ["modules"]
                     },
                     "porechop/porechop": {
@@ -214,7 +214,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index 16bccc9..67f497e 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -2,17 +2,17 @@ process UNTAR {
     tag "$archive"
     label 'process_single'
 
-    conda "conda-forge::sed=4.7"
+    conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'ubuntu:20.04' }"
+        'docker.io/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(archive)
 
     output:
-    tuple val(meta), path("$untar"), emit: untar
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path("$prefix"), emit: untar
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,31 +20,29 @@ process UNTAR {
     script:
     def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    untar     = archive.toString() - '.tar.gz'
+    prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
 
     """
-    mkdir output
+    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 output
-    if [[ \$(tar -tzf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+    ## 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 output --strip-components 1 \\
-            -xzvf \\
+            -C $prefix --strip-components 1 \\
+            -xavf \\
             $args \\
             $archive \\
             $args2
     else
         tar \\
-            -C output \\
-            -xzvf \\
+            -C $prefix \\
+            -xavf \\
             $args \\
             $archive \\
             $args2
     fi
 
-    mv output ${untar}
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
@@ -52,9 +50,10 @@ process UNTAR {
     """
 
     stub:
-    untar     = archive.toString() - '.tar.gz'
+    prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
     """
-    touch $untar
+    mkdir $prefix
+    touch ${prefix}/file.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
index ea7a3f3..db241a6 100644
--- a/modules/nf-core/untar/meta.yml
+++ b/modules/nf-core/untar/meta.yml
@@ -3,6 +3,7 @@ description: Extract files.
 keywords:
   - untar
   - uncompress
+  - extract
 tools:
   - untar:
       description: |