From fa212b2faa697829ffe24db1d816d827d60e2f44 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 4 Oct 2023 09:26:35 +0200 Subject: [PATCH 1/3] revert controlfreec-assesssignificance --- modules.json | 3 ++- .../controlfreec-assesssignificance.diff | 19 +++++++++++++++++++ .../controlfreec/assesssignificance/main.nf | 6 +++--- 3 files changed, 24 insertions(+), 4 deletions(-) create mode 100644 modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff diff --git a/modules.json b/modules.json index 222ad3782d..84b30a76dc 100644 --- a/modules.json +++ b/modules.json @@ -78,7 +78,8 @@ "controlfreec/assesssignificance": { "branch": "master", "git_sha": "3fbcafe2543dabcc7b2be0f3b24507002b3e4b0d", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff" }, "controlfreec/freec": { "branch": "master", diff --git a/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff b/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff new file mode 100644 index 0000000000..a80891d309 --- /dev/null +++ b/modules/nf-core/controlfreec/assesssignificance/controlfreec-assesssignificance.diff @@ -0,0 +1,19 @@ +Changes in module 'nf-core/controlfreec/assesssignificance' +--- modules/nf-core/controlfreec/assesssignificance/main.nf ++++ modules/nf-core/controlfreec/assesssignificance/main.nf +@@ -2,10 +2,10 @@ + tag "$meta.id" + label 'process_low' + +- conda "bioconda::control-freec=11.6b" ++ conda "bioconda::control-freec=11.6" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' : +- 'biocontainers/control-freec:11.6b--hdbdd923_0' }" ++ 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1' : ++ 'biocontainers/control-freec:11.6--h1b792b2_1' }" + + input: + tuple val(meta), path(cnvs), path(ratio) + +************************************************************ diff --git a/modules/nf-core/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf index aada1c4a49..8c5cd42b41 100644 --- a/modules/nf-core/controlfreec/assesssignificance/main.nf +++ b/modules/nf-core/controlfreec/assesssignificance/main.nf @@ -2,10 +2,10 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE { tag "$meta.id" label 'process_low' - conda "bioconda::control-freec=11.6b" + conda "bioconda::control-freec=11.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' : - 'biocontainers/control-freec:11.6b--hdbdd923_0' }" + 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1' : + 'biocontainers/control-freec:11.6--h1b792b2_1' }" input: tuple val(meta), path(cnvs), path(ratio) From 547a1a45d63819604e0c127a31dd32ee5243c38e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 4 Oct 2023 09:28:26 +0200 Subject: [PATCH 2/3] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 64a0a28273..4444c541de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ Ráhpajávvre is the Lule Sámi spelling of Rapaselet. - [#1247](https://github.com/nf-core/sarek/pull/1247) - FIX: Result paths for full size test to be correctly displayed on the website - [#1256](https://github.com/nf-core/sarek/pull/1256) - Fix issue with controlfreec container declaration +- [#1270](https://github.com/nf-core/sarek/pull/1270) - Revert controlfreec/assesssignificance module to 11.6 ### Dependencies From b84b8b5df8952bc2f5827eb50b33a4a3f8f553fe Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 4 Oct 2023 09:36:09 +0200 Subject: [PATCH 3/3] update dependencies table --- CHANGELOG.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4444c541de..bda739b522 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,8 +27,9 @@ Ráhpajávvre is the Lule Sámi spelling of Rapaselet. ### Dependencies -| Dependency | Old version | New version | -| ---------- | ----------- | ----------- | +| Dependency | Old version | New version | +| -------------------------------- | ----------- | ----------- | +| Control-FREEC/assesssignificance | 11.6b | 11.6 | ## [3.3.1](https://github.com/nf-core/sarek/releases/tag/3.3.1) - Biellorippjávrre