Merge pull request #315 from jfy133/base-container-image-update

Base container image update
nf-core · Jun 3, 2022 · 18a8634 · 18a8634
2 parents 91e9843 + c666942
commit 18a8634
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Showing 12 changed files with 22 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#286](https://github.com/nf-core/mag/pull/286) - Cite our publication instead of the preprint
 - [#291](https://github.com/nf-core/mag/pull/291), [#299](https://github.com/nf-core/mag/pull/299) - Add extra results folder `GenomeBinning/depths/contigs` for `[assembler]-[sample/group]-depth.txt.gz`, and `GenomeBinning/depths/bins` for `bin_depths_summary.tsv` and `[assembler]-[binner]-[sample/group]-binDepths.heatmap.png`
 - [#302](https://github.com/nf-core/mag/pull/302) - Update to nf-core 2.4 `TEMPLATE`
+- [#315](https://github.com/nf-core/mag/pull/315) - Replace base container for standard shell tools to fix problems with running on Google Cloud
 
 ### `Fixed`
 

diff --git a/modules.json b/modules.json
@@ -34,7 +34,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gunzip": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
             },
             "maxbin2": {
                 "git_sha": "b78a4a456762a4c59fd5023e70f36a27f76d4a97"

diff --git a/modules/local/busco_db_preparation.nf b/modules/local/busco_db_preparation.nf
@@ -3,8 +3,8 @@ process BUSCO_DB_PREPARATION {
 
     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:
     path database

diff --git a/modules/local/busco_save_download.nf b/modules/local/busco_save_download.nf
@@ -4,8 +4,8 @@ process BUSCO_SAVE_DOWNLOAD {
 
     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:
     path(busco_downloads)

diff --git a/modules/local/cat_db.nf b/modules/local/cat_db.nf
@@ -3,8 +3,8 @@ process CAT_DB {
 
     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:
     path(database)

diff --git a/modules/local/centrifuge_db_preparation.nf b/modules/local/centrifuge_db_preparation.nf
@@ -2,8 +2,8 @@ process CENTRIFUGE_DB_PREPARATION {
 
     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:
     path db

diff --git a/modules/local/gtdbtk_db_preparation.nf b/modules/local/gtdbtk_db_preparation.nf
@@ -3,8 +3,8 @@ process GTDBTK_DB_PREPARATION {
 
     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:
     path(database)

diff --git a/modules/local/kraken2_db_preparation.nf b/modules/local/kraken2_db_preparation.nf
@@ -2,8 +2,8 @@ process KRAKEN2_DB_PREPARATION {
 
     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:
     path db

diff --git a/modules/local/pool_paired_reads.nf b/modules/local/pool_paired_reads.nf
@@ -3,8 +3,8 @@ process POOL_PAIRED_READS {
 
     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(reads1), path(reads2)

diff --git a/modules/local/pool_single_reads.nf b/modules/local/pool_single_reads.nf
@@ -3,8 +3,8 @@ process POOL_SINGLE_READS {
 
     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(reads)

diff --git a/modules/local/quast_bins_summary.nf b/modules/local/quast_bins_summary.nf
@@ -2,8 +2,8 @@ process QUAST_BINS_SUMMARY {
 
     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:
     path(summaries)

diff --git a/modules/nf-core/modules/gunzip/main.nf b/modules/nf-core/modules/gunzip/main.nf