From d89b14291ac6d02864c98387898f592c5d7027a2 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 19 Oct 2023 09:11:48 +0100 Subject: [PATCH 1/5] Bump shinyngs versions --- conf/modules.config | 4 ++-- modules.json | 8 ++++---- modules/nf-core/shinyngs/app/main.nf | 6 +++--- modules/nf-core/shinyngs/staticdifferential/main.nf | 6 +++--- modules/nf-core/shinyngs/staticexploratory/main.nf | 6 +++--- modules/nf-core/shinyngs/validatefomcomponents/main.nf | 6 +++--- 6 files changed, 18 insertions(+), 18 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 60e0629d..3245195e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -390,8 +390,8 @@ process { } withName: RMARKDOWNNOTEBOOK { - conda = "bioconda::r-shinyngs=1.8.2" - container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.2--r43hdfd78af_0' : 'quay.io/biocontainers/r-shinyngs:1.8.2--r43hdfd78af_0' }" } + conda "bioconda::r-shinyngs=1.8.4" + container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" } publishDir = [ path: { "${params.outdir}/report" }, mode: params.publish_dir_mode, diff --git a/modules.json b/modules.json index c6fce10f..102495bb 100644 --- a/modules.json +++ b/modules.json @@ -72,22 +72,22 @@ }, "shinyngs/app": { "branch": "master", - "git_sha": "707c31e838cb77198e30d8eeb138728ce09a4dd2", + "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b", "installed_by": ["modules"] }, "shinyngs/staticdifferential": { "branch": "master", - "git_sha": "022afb76b0fc7e304b0061a648f8f6cef03bba95", + "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b", "installed_by": ["modules"] }, "shinyngs/staticexploratory": { "branch": "master", - "git_sha": "022afb76b0fc7e304b0061a648f8f6cef03bba95", + "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b", "installed_by": ["modules"] }, "shinyngs/validatefomcomponents": { "branch": "master", - "git_sha": "022afb76b0fc7e304b0061a648f8f6cef03bba95", + "git_sha": "1b2fa2138849ac09b3d5c1e25ed70650ec1ebd7b", "installed_by": ["modules"] }, "untar": { diff --git a/modules/nf-core/shinyngs/app/main.nf b/modules/nf-core/shinyngs/app/main.nf index 60ea6a79..9cdf5cb1 100644 --- a/modules/nf-core/shinyngs/app/main.nf +++ b/modules/nf-core/shinyngs/app/main.nf @@ -13,10 +13,10 @@ process SHINYNGS_APP { // // Those values must then be set in your Nextflow secrets. - conda "bioconda::r-shinyngs=1.8.1" + conda "bioconda::r-shinyngs=1.8.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.1--r43hdfd78af_0' : - 'biocontainers/r-shinyngs:1.8.1--r43hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : + 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" input: tuple val(meta), path(sample), path(feature_meta), path(assay_files) // Experiment-level info diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf index d2bbbc8c..e25edf5b 100644 --- a/modules/nf-core/shinyngs/staticdifferential/main.nf +++ b/modules/nf-core/shinyngs/staticdifferential/main.nf @@ -2,10 +2,10 @@ process SHINYNGS_STATICDIFFERENTIAL { tag "$meta.id" label 'process_single' - conda "bioconda::r-shinyngs=1.8.2" + conda "bioconda::r-shinyngs=1.8.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.2--r43hdfd78af_0' : - 'biocontainers/r-shinyngs:1.8.2--r43hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : + 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" input: tuple val(meta), path(differential_result) // Differential info: contrast and differential stats diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf index 851325bf..4f5cbc33 100644 --- a/modules/nf-core/shinyngs/staticexploratory/main.nf +++ b/modules/nf-core/shinyngs/staticexploratory/main.nf @@ -2,10 +2,10 @@ process SHINYNGS_STATICEXPLORATORY { tag "$meta.id" label 'process_single' - conda "bioconda::r-shinyngs=1.8.2" + conda "bioconda::r-shinyngs=1.8.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.2--r43hdfd78af_0' : - 'biocontainers/r-shinyngs:1.8.2--r43hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : + 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" input: tuple val(meta), path(sample), path(feature_meta), path(assay_files) diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf index bdfb19af..0e63c89a 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/main.nf +++ b/modules/nf-core/shinyngs/validatefomcomponents/main.nf @@ -2,10 +2,10 @@ process SHINYNGS_VALIDATEFOMCOMPONENTS { tag "$sample" label 'process_single' - conda "bioconda::r-shinyngs=1.8.2" + conda "bioconda::r-shinyngs=1.8.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.2--r43hdfd78af_0' : - 'biocontainers/r-shinyngs:1.8.2--r43hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : + 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" input: tuple val(meta), path(sample), path(assay_files) From 0c901915014e15a8ae6521cf711d02a20fb2b1c9 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 19 Oct 2023 09:16:55 +0100 Subject: [PATCH 2/5] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ba5a0ac6..bc0b398f 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 - [[#119](https://github.com/nf-core/differentialabundance/issues/119)] - Document sample sheet for Affy arrays ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) - [[#165](https://github.com/nf-core/differentialabundance/issues/165)] - Update subway map ([@pinin4fjords](https://github.com/pinin4fjords), review by [@FriederikeHanssen](https://github.com/FriederikeHanssen)) - [[#135](https://github.com/nf-core/differentialabundance/issues/135)] - workaround OPENBLAS using all cores problem ([@pinin4fjords](https://github.com/pinin4fjords), review by [@sateeshperi](https://github.com/sateeshperi)) +- [[#176](https://github.com/nf-core/differentialabundance/pull/176)] - bump shinyngs ([@pinin4fjords](https://github.com/pinin4fjords), review by ) ### `Fixed` From e8a5519cf3250e158ed7fe71161c10fb881fa848 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 19 Oct 2023 09:17:37 +0100 Subject: [PATCH 3/5] poke CI --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bc0b398f..e6aba493 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 - [[#119](https://github.com/nf-core/differentialabundance/issues/119)] - Document sample sheet for Affy arrays ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) - [[#165](https://github.com/nf-core/differentialabundance/issues/165)] - Update subway map ([@pinin4fjords](https://github.com/pinin4fjords), review by [@FriederikeHanssen](https://github.com/FriederikeHanssen)) - [[#135](https://github.com/nf-core/differentialabundance/issues/135)] - workaround OPENBLAS using all cores problem ([@pinin4fjords](https://github.com/pinin4fjords), review by [@sateeshperi](https://github.com/sateeshperi)) -- [[#176](https://github.com/nf-core/differentialabundance/pull/176)] - bump shinyngs ([@pinin4fjords](https://github.com/pinin4fjords), review by ) +- [[#176](https://github.com/nf-core/differentialabundance/pull/176)] - bump shinyngs ([@pinin4fjords](https://github.com/pinin4fjords), review by ) ### `Fixed` From 6ff143091cfad642c2353d44c88133faede8291e Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 19 Oct 2023 09:20:03 +0100 Subject: [PATCH 4/5] Correct conda setting --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 3245195e..8b3b66e7 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -390,7 +390,7 @@ process { } withName: RMARKDOWNNOTEBOOK { - conda "bioconda::r-shinyngs=1.8.4" + conda = "bioconda::r-shinyngs=1.8.4" container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" } publishDir = [ path: { "${params.outdir}/report" }, From a321afa8b15fdc043f372e180e9f342b0cacab77 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 19 Oct 2023 08:21:33 +0000 Subject: [PATCH 5/5] [automated] Fix linting with Prettier --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e6aba493..bc0b398f 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 - [[#119](https://github.com/nf-core/differentialabundance/issues/119)] - Document sample sheet for Affy arrays ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) - [[#165](https://github.com/nf-core/differentialabundance/issues/165)] - Update subway map ([@pinin4fjords](https://github.com/pinin4fjords), review by [@FriederikeHanssen](https://github.com/FriederikeHanssen)) - [[#135](https://github.com/nf-core/differentialabundance/issues/135)] - workaround OPENBLAS using all cores problem ([@pinin4fjords](https://github.com/pinin4fjords), review by [@sateeshperi](https://github.com/sateeshperi)) -- [[#176](https://github.com/nf-core/differentialabundance/pull/176)] - bump shinyngs ([@pinin4fjords](https://github.com/pinin4fjords), review by ) +- [[#176](https://github.com/nf-core/differentialabundance/pull/176)] - bump shinyngs ([@pinin4fjords](https://github.com/pinin4fjords), review by ) ### `Fixed`