From 14e76774942a3fe4c9837541af5edb8457cc640c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Oct 2024 09:48:38 +0200 Subject: [PATCH 1/2] force convert for some singularity images --- .../nf-core/bedtools/genomecov/bedtools-genomecov.diff | 10 ++++++---- modules/nf-core/bedtools/genomecov/main.nf | 4 +--- modules/nf-core/cat/fastq/cat-fastq.diff | 10 ++++++---- modules/nf-core/cat/fastq/main.nf | 4 +--- modules/nf-core/sortmerna/main.nf | 4 +--- modules/nf-core/sortmerna/sortmerna.diff | 8 ++++---- modules/nf-core/star/align/main.nf | 4 +--- modules/nf-core/star/align/star-align.diff | 10 ++++++---- modules/nf-core/star/genomegenerate/main.nf | 4 +--- .../star/genomegenerate/star-genomegenerate.diff | 10 ++++++---- 10 files changed, 33 insertions(+), 35 deletions(-) diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff index bb848b16f..17aa9eb2d 100644 --- a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -2,12 +2,14 @@ Changes in module 'nf-core/bedtools/genomecov' Changes in 'bedtools/genomecov/main.nf': --- modules/nf-core/bedtools/genomecov/main.nf +++ modules/nf-core/bedtools/genomecov/main.nf -@@ -5,7 +5,7 @@ +@@ -3,9 +3,7 @@ + label 'process_single' + conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" -+ 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" ++ container 'nf-core/bedtools_coreutils:a623c13f66d5262b' input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 91869ec23..10a99d439 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,9 +3,7 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': - 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" + container 'nf-core/bedtools_coreutils:a623c13f66d5262b' input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/cat/fastq/cat-fastq.diff b/modules/nf-core/cat/fastq/cat-fastq.diff index debb8944b..0d3832c04 100644 --- a/modules/nf-core/cat/fastq/cat-fastq.diff +++ b/modules/nf-core/cat/fastq/cat-fastq.diff @@ -3,12 +3,14 @@ Changes in module 'nf-core/cat/fastq' Changes in 'cat/fastq/main.nf': --- modules/nf-core/cat/fastq/main.nf +++ modules/nf-core/cat/fastq/main.nf -@@ -5,7 +5,7 @@ +@@ -3,9 +3,7 @@ + label 'process_single' + conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : - 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' }" -+ 'nf-core/coreutils:9.5--ae99c88a9b28c264' }" ++ container 'nf-core/coreutils:9.5--ae99c88a9b28c264' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index f2848aa6e..6f4f96e34 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -3,9 +3,7 @@ process CAT_FASTQ { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c2/c262fc09eca59edb5a724080eeceb00fb06396f510aefb229c2d2c6897e63975/data' : - 'nf-core/coreutils:9.5--ae99c88a9b28c264' }" + container 'nf-core/coreutils:9.5--ae99c88a9b28c264' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/sortmerna/main.nf b/modules/nf-core/sortmerna/main.nf index b479f0459..2ea221c59 100644 --- a/modules/nf-core/sortmerna/main.nf +++ b/modules/nf-core/sortmerna/main.nf @@ -3,9 +3,7 @@ process SORTMERNA { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' : - 'nf-core/sortmerna:4.3.7--6502243397c065ba' }" + container 'nf-core/sortmerna:4.3.7--6502243397c065ba' input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sortmerna/sortmerna.diff b/modules/nf-core/sortmerna/sortmerna.diff index 187650b2a..5e37cabf8 100644 --- a/modules/nf-core/sortmerna/sortmerna.diff +++ b/modules/nf-core/sortmerna/sortmerna.diff @@ -3,14 +3,14 @@ Changes in module 'nf-core/sortmerna' Changes in 'sortmerna/main.nf': --- modules/nf-core/sortmerna/main.nf +++ modules/nf-core/sortmerna/main.nf -@@ -4,8 +4,8 @@ +@@ -3,9 +3,7 @@ + label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.6--h9ee0642_0' : - 'biocontainers/sortmerna:4.3.6--h9ee0642_0' }" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/15/15b50826336c394eab2bf6d731f00729921598ffc6463278da6316e768b16b8b/data' : -+ 'nf-core/sortmerna:4.3.7--6502243397c065ba' }" ++ container 'nf-core/sortmerna:4.3.7--6502243397c065ba' input: tuple val(meta), path(reads) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index b5d2fbd58..eadddb03f 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -3,9 +3,7 @@ process STAR_ALIGN { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" + container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/align/star-align.diff b/modules/nf-core/star/align/star-align.diff index 84e65ca00..ea28fb1aa 100644 --- a/modules/nf-core/star/align/star-align.diff +++ b/modules/nf-core/star/align/star-align.diff @@ -2,12 +2,14 @@ Changes in module 'nf-core/star/align' Changes in 'star/align/main.nf': --- modules/nf-core/star/align/main.nf +++ modules/nf-core/star/align/main.nf -@@ -5,7 +5,7 @@ +@@ -3,9 +3,7 @@ + label 'process_high' + conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" -+ 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" ++ container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index bdd1d0db0..af72f920b 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -3,9 +3,7 @@ process STAR_GENOMEGENERATE { label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" + container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff index 515dd1bac..dea48619b 100644 --- a/modules/nf-core/star/genomegenerate/star-genomegenerate.diff +++ b/modules/nf-core/star/genomegenerate/star-genomegenerate.diff @@ -2,12 +2,14 @@ Changes in module 'nf-core/star/genomegenerate' Changes in 'star/genomegenerate/main.nf': --- modules/nf-core/star/genomegenerate/main.nf +++ modules/nf-core/star/genomegenerate/main.nf -@@ -5,7 +5,7 @@ +@@ -3,9 +3,7 @@ + label 'process_high' + conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b4/b425bc2a95806d878993f9a66dae3ae80ac2dafff4c208c5ae01b7a90a32fa91/data' : - 'community.wave.seqera.io/library/star_samtools_htslib_gawk:10c6e8c834460019' }" -+ 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' }" ++ container 'nf-core/star_samtools_htslib_gawk:10c6e8c834460019' input: tuple val(meta), path(fasta) From cb5cc2c3f035dddf9b54ac22ca38bcf1a2475365 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 24 Oct 2024 10:16:20 +0200 Subject: [PATCH 2/2] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d87588c9c..39e77a767 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ Special thanks to the following for their contributions to the release: - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix - [PR #1440](https://github.com/nf-core/rnaseq/pull/1440) - Further reduce matrix +- [PR #1441](https://github.com/nf-core/rnaseq/pull/1441) - Force some containers to be converted from docker to singularity to fix nf-core download tests ### Software dependencies