From dab41f443be006145e55c600cd48ee4f529a6073 Mon Sep 17 00:00:00 2001 From: Peter Kneale Date: Wed, 25 Feb 2026 02:14:20 +0000 Subject: [PATCH 1/2] module update: subread/featurecounts - Bump container versions #10249 --- modules/nf-core/subread/featurecounts/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 1ffcbf54d733..8067dba17cf0 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -4,8 +4,8 @@ process SUBREAD_FEATURECOUNTS { conda "${moduleDir}/environment.yml" container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://depot.galaxyproject.org/singularity/subread:2.0.6--he4a0461_2' - : 'biocontainers/subread:2.0.6--he4a0461_2'}" + ? 'https://depot.galaxyproject.org/singularity/subread:2.1.1--h577a1d6_0' + : 'biocontainers/subread:2.1.1--h577a1d6_0'}" input: tuple val(meta), path(bams), path(annotation) From 4736ab3afc0317640636de89d5ee7c81e6b7ad47 Mon Sep 17 00:00:00 2001 From: Peter Kneale Date: Thu, 26 Feb 2026 03:46:45 +0000 Subject: [PATCH 2/2] Bump environment.yml and update test snapshots --- .../subread/featurecounts/environment.yml | 2 +- .../featurecounts/tests/main.nf.test.snap | 72 +++++++++---------- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 157752509611..231335592777 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::subread=2.0.6 + - bioconda::subread=2.1.1 diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap index 145d49b8f251..fb98cfee99ac 100644 --- a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "single_end": true, "strandedness": "forward" }, - "test.featureCounts.tsv:md5,21ff44bfaa4a3d8e8b7e749078f7a201" + "test.featureCounts.tsv:md5,af5abde30c52606302d64a3f960a262a" ] ], [ @@ -26,16 +26,16 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ] } ], + "timestamp": "2026-02-26T03:28:13.8156532", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T14:44:54.308461465" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [bam] - forward - stub": { "content": [ @@ -64,7 +64,7 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ], "counts": [ @@ -91,16 +91,16 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ] } ], + "timestamp": "2026-02-26T03:28:21.127211404", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T14:44:59.542545235" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [bam] - unstranded": { "content": [ @@ -111,7 +111,7 @@ "single_end": true, "strandedness": "unstranded" }, - "test.featureCounts.tsv:md5,9474f78d2d1d43613cbc16c10ba15047" + "test.featureCounts.tsv:md5,355c22823290c40ccadeee94a21eca8b" ] ], [ @@ -129,16 +129,16 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ] } ], + "timestamp": "2026-02-26T03:28:43.068113331", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T14:45:15.194324716" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [bam] - reverse - stub": { "content": [ @@ -167,7 +167,7 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ], "counts": [ @@ -194,16 +194,16 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ] } ], + "timestamp": "2026-02-26T03:28:35.854492757", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T14:45:09.979159361" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [bam] - reverse": { "content": [ @@ -214,7 +214,7 @@ "single_end": true, "strandedness": "reverse" }, - "test.featureCounts.tsv:md5,7df6092fdc65ce40b71c64e0c97f95c6" + "test.featureCounts.tsv:md5,e79027ec5752cfdd6e8d85bb6932294c" ] ], [ @@ -232,16 +232,16 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ] } ], + "timestamp": "2026-02-26T03:28:28.511647205", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T14:45:04.836250949" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "sarscov2 [bam] - unstranded - stub": { "content": [ @@ -270,7 +270,7 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ], "counts": [ @@ -297,15 +297,15 @@ [ "SUBREAD_FEATURECOUNTS", "subread", - "2.0.6" + "2.1.1" ] ] } ], + "timestamp": "2026-02-26T03:28:50.377997465", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T14:45:20.368253962" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file