Replace gawk containers with ubuntu

nf-core · May 27, 2022 · c48d547 · c48d547
1 parent 5165e83
commit c48d547
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Showing 5 changed files with 15 additions and 15 deletions.
diff --git a/modules/local/export_meta.nf b/modules/local/export_meta.nf
@@ -1,10 +1,10 @@
 process EXPORT_META {
     label 'process_min'
 
-    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'quay.io/biocontainers/gawk:5.1.0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     val meta

diff --git a/modules/local/linux/awk.nf b/modules/local/linux/awk.nf
@@ -2,10 +2,10 @@ process AWK {
     tag "$meta.id"
     label 'process_ultralow'
 
-    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/local/linux/awk_script.nf b/modules/local/linux/awk_script.nf
@@ -2,10 +2,10 @@ process AWK_SCRIPT {
     tag "$meta.id"
     label 'process_min'
 
-    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'quay.io/biocontainers/gawk:5.1.0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/local/linux/cut.nf b/modules/local/linux/cut.nf
@@ -2,10 +2,10 @@ process CUT {
     tag "$meta.id"
     label 'process_min'
 
-    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'quay.io/biocontainers/gawk:5.1.0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/local/linux/sort.nf b/modules/local/linux/sort.nf
@@ -2,10 +2,10 @@ process SORT {
     tag "$meta.id"
     label 'process_ultralow'
 
-    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'quay.io/biocontainers/gawk:5.1.0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(input)