Merge pull request #199 from skrakau/add_and_fix_container

Add and fix container
nf-core · May 26, 2021 · 0de4b58 · 0de4b58
2 parents 9ee55e4 + bbae7e0
commit 0de4b58
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Showing 3 changed files with 20 additions and 2 deletions.
diff --git a/modules/local/busco_save_download.nf b/modules/local/busco_save_download.nf
@@ -14,6 +14,13 @@ process BUSCO_SAVE_DOWNLOAD {
         overwrite: false,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
+
     input:
     path(busco_downloads)
 

diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
@@ -11,8 +11,12 @@ process GET_SOFTWARE_VERSIONS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', publish_id:'') }
 
-    conda     (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    container "quay.io/biocontainers/python:3.8.3"
+    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
+    } else {
+        container "quay.io/biocontainers/python:3.8.3"
+    }
 
     cache false
 

diff --git a/modules/local/quast_bins_summary.nf b/modules/local/quast_bins_summary.nf
@@ -10,6 +10,13 @@ process QUAST_BINS_SUMMARY {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
+    } else {
+        container "biocontainers/biocontainers:v1.2.0_cv1"
+    }
+
     input:
     path(summaries)