From f6522c801ad9884b49f5ddc02e18486e6caba86b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 30 Sep 2024 14:43:47 +0200 Subject: [PATCH 1/3] patch bedtools/genomecov to use quay.io to solve issue with nf-core download --- CHANGELOG.md | 1 + modules.json | 3 +- .../genomecov/bedtools-genomecov.diff | 37 +++++++++++++++++++ modules/nf-core/bedtools/genomecov/main.nf | 4 +- 4 files changed, 41 insertions(+), 4 deletions(-) create mode 100644 modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff diff --git a/CHANGELOG.md b/CHANGELOG.md index d2797457d..a4adf8bdb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [PR #1386](https://github.com/nf-core/rnaseq/pull/1386) - Bump pipeline version to 3.16.0dev - [PR #1388](https://github.com/nf-core/rnaseq/pull/1388) - Adding Kraken2/Bracken on unaligned reads as an additional quality control step to detect sample contamination - [PR #1389](https://github.com/nf-core/rnaseq/pull/1389) - Update animated subway map +- [PR #1393](https://github.com/nf-core/rnaseq/pull/1393) - Use quay.io for bedtools/genomecov to solve issue with nf-core download ### Parameters diff --git a/modules.json b/modules.json index 4c9ba76f1..c351786e2 100644 --- a/modules.json +++ b/modules.json @@ -13,7 +13,8 @@ "bedtools/genomecov": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff" }, "bracken/bracken": { "branch": "master", diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff new file mode 100644 index 000000000..02fdbd053 --- /dev/null +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -0,0 +1,37 @@ +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 +@@ -3,9 +3,7 @@ + label 'process_single' + + conda "${moduleDir}/environment.yml" +- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': +- 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" ++ container 'nf-core/bedtools_coreutils:a623c13f66d5262b' + + input: + tuple val(meta), path(intervals), val(scale) + +'modules/nf-core/bedtools/genomecov/meta.yml' is unchanged +'modules/nf-core/bedtools/genomecov/environment.yml' is unchanged +'modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap' is unchanged +'modules/nf-core/bedtools/genomecov/tests/nextflow.config' is unchanged +Changes in 'bedtools/genomecov/tests/main.nf.test': +--- modules/nf-core/bedtools/genomecov/tests/main.nf.test ++++ modules/nf-core/bedtools/genomecov/tests/main.nf.test +@@ -3,11 +3,6 @@ + script "../main.nf" + process "BEDTOOLS_GENOMECOV" + config "./nextflow.config" +- +- tag "modules" +- tag "modules_nfcore" +- tag "bedtools" +- tag "bedtools/genomecov" + + test("sarscov2 - no scale") { + when { + +************************************************************ diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 8403c5303..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 ? - 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" + container 'nf-core/bedtools_coreutils:a623c13f66d5262b' input: tuple val(meta), path(intervals), val(scale) From 5c61ed3490988b384beae45e3e73609b7974924f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 30 Sep 2024 14:50:50 +0200 Subject: [PATCH 2/3] use url for singularity --- .../nf-core/bedtools/genomecov/bedtools-genomecov.diff | 8 ++++---- modules/nf-core/bedtools/genomecov/main.nf | 4 +++- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff index 02fdbd053..6475cdda5 100644 --- a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -2,14 +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 -@@ -3,9 +3,7 @@ - label 'process_single' +@@ -4,8 +4,8 @@ conda "${moduleDir}/environment.yml" -- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" -+ container 'nf-core/bedtools_coreutils:a623c13f66d5262b' ++ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21': ++ 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: tuple val(meta), path(intervals), val(scale) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 10a99d439..60d7d9e20 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -3,7 +3,9 @@ process BEDTOOLS_GENOMECOV { label 'process_single' conda "${moduleDir}/environment.yml" - container 'nf-core/bedtools_coreutils:a623c13f66d5262b' + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21': + 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: tuple val(meta), path(intervals), val(scale) From 894a770a06b3f09f7f8188f3505e88578605c01d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 30 Sep 2024 14:53:01 +0200 Subject: [PATCH 3/3] use proper url for singularity --- modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff | 2 +- modules/nf-core/bedtools/genomecov/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff index 6475cdda5..53d7e34df 100644 --- a/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff +++ b/modules/nf-core/bedtools/genomecov/bedtools-genomecov.diff @@ -8,7 +8,7 @@ Changes in 'bedtools/genomecov/main.nf': container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': - 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" -+ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21': ++ 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': + 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 60d7d9e20..91869ec23 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_GENOMECOV { 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': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': 'nf-core/bedtools_coreutils:a623c13f66d5262b' }" input: