From a5dc5cc49c814b090375ebede7b62188d728389b Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 3 Jun 2022 08:44:50 +0200 Subject: [PATCH 1/4] Replace busybox with Ubuntu base image for GCP support --- modules.json | 2 +- modules/local/busco_db_preparation.nf | 4 ++-- modules/local/busco_save_download.nf | 4 ++-- modules/local/centrifuge_db_preparation.nf | 4 ++-- modules/local/gtdbtk_db_preparation.nf | 4 ++-- modules/local/kraken2_db_preparation.nf | 4 ++-- modules/local/pool_paired_reads.nf | 4 ++-- modules/local/pool_single_reads.nf | 4 ++-- modules/local/quast_bins_summary.nf | 4 ++-- modules/nf-core/modules/gunzip/main.nf | 4 ++-- 10 files changed, 19 insertions(+), 19 deletions(-) diff --git a/modules.json b/modules.json index f09b78c5..c1f58a4d 100644 --- 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 index 9b8de4e3..9d655a02 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: path database diff --git a/modules/local/busco_save_download.nf b/modules/local/busco_save_download.nf index 839cc7da..63928f85 100644 --- a/modules/local/busco_save_download.nf +++ b/modules/local/busco_save_download.nf @@ -4,8 +4,8 @@ process BUSCO_SAVE_DOWNLOAD { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ 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/centrifuge_db_preparation.nf b/modules/local/centrifuge_db_preparation.nf index 2f1f7c04..f1a99afe 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: path db diff --git a/modules/local/gtdbtk_db_preparation.nf b/modules/local/gtdbtk_db_preparation.nf index f2d79053..aabd1e0a 100644 --- a/modules/local/gtdbtk_db_preparation.nf +++ b/modules/local/gtdbtk_db_preparation.nf @@ -3,8 +3,8 @@ process GTDBTK_DB_PREPARATION { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ 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 index 81c294a8..38202110 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: path db diff --git a/modules/local/pool_paired_reads.nf b/modules/local/pool_paired_reads.nf index ac7fcb68..27c5e0f3 100644 --- a/modules/local/pool_paired_reads.nf +++ b/modules/local/pool_paired_reads.nf @@ -3,8 +3,8 @@ process POOL_PAIRED_READS { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ 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 index ac165082..cc633d4a 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(reads) diff --git a/modules/local/quast_bins_summary.nf b/modules/local/quast_bins_summary.nf index 933758fb..eae5ef78 100644 --- a/modules/local/quast_bins_summary.nf +++ b/modules/local/quast_bins_summary.nf @@ -2,8 +2,8 @@ process QUAST_BINS_SUMMARY { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ 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 index 9d4b0666..61bf1afa 100644 --- a/modules/nf-core/modules/gunzip/main.nf +++ b/modules/nf-core/modules/gunzip/main.nf @@ -4,8 +4,8 @@ process GUNZIP { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' : - 'biocontainers/biocontainers:v1.2.0_cv1' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(archive) From c1a30cdbb6202feda7d242c9b4795f05cd9b0971 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 3 Jun 2022 08:47:53 +0200 Subject: [PATCH 2/4] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c0c1b275..a147f8ab 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#286](https://github.com/nf-core/mag/pull/286) - Cite our publication instead of the preprint - [#299](https://github.com/nf-core/mag/pull/299) - Add extra results folder `GenomeBinning/depths` for `[assembler]-[sample/group]-depth.txt.gz`, `bin_depths_summary.tsv` and `[assembler]-[binner]-[sample/group]-binDepths.heatmap.png` - [#302](https://github.com/nf-core/mag/pull/302) - Update to nf-core 2.4 `TEMPLATE` +- Replace base container for standard shell tools to fix problems with running on Google Cloud ### `Fixed` From 152c1b0d5430863c86fb7e0758846514548f5ffa Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 3 Jun 2022 08:58:50 +0200 Subject: [PATCH 3/4] Add missing file --- modules/local/cat_db.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/cat_db.nf b/modules/local/cat_db.nf index 3642c939..03f463c9 100644 --- a/modules/local/cat_db.nf +++ b/modules/local/cat_db.nf @@ -3,8 +3,8 @@ process CAT_DB { conda (params.enable_conda ? "conda-forge::sed=4.7" : null) container "${ 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) From c666942dedebc4ec16ffd6a776d5b6466f7ec15c Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 3 Jun 2022 11:34:56 +0200 Subject: [PATCH 4/4] Update CHANGELOG.md Co-authored-by: Sabrina Krakau --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a147f8ab..17650e93 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +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 - [#299](https://github.com/nf-core/mag/pull/299) - Add extra results folder `GenomeBinning/depths` for `[assembler]-[sample/group]-depth.txt.gz`, `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` -- Replace base container for standard shell tools to fix problems with running on Google Cloud +- [#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`