From c28c1018e8ecec1b73bc93ac1669382ef9217014 Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 8 Feb 2024 08:31:33 +0100 Subject: [PATCH] GSEA update --- CHANGELOG.md | 1 + modules.json | 2 +- modules/nf-core/gsea/gsea/environment.yml | 1 + modules/nf-core/gsea/gsea/main.nf | 4 ++-- modules/nf-core/gsea/gsea/meta.yml | 2 +- 5 files changed, 6 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cd7aa2a8..49736ab7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [[#231](https://github.com/nf-core/differentialabundance/pull/231) - Update GSEA module to fix butterfly plot bug ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#226](https://github.com/nf-core/differentialabundance/pull/226) - Fix DESEQ2_NORM in modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) - [[#221](https://github.com/nf-core/differentialabundance/pull/221) - Update shinyngs modules to address density plots issue ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse)) - [[#223](https://github.com/nf-core/differentialabundance/pull/223)] - tabulartogseacls fixes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse)) diff --git a/modules.json b/modules.json index 0c0f4120..75f6a7ea 100644 --- a/modules.json +++ b/modules.json @@ -52,7 +52,7 @@ }, "gsea/gsea": { "branch": "master", - "git_sha": "516189e968feb4ebdd9921806988b4c12b4ac2dc", + "git_sha": "7aa7ced253469386f0645133ec3e838098dbe67c", "installed_by": ["modules"] }, "gunzip": { diff --git a/modules/nf-core/gsea/gsea/environment.yml b/modules/nf-core/gsea/gsea/environment.yml index 3158f736..cb3c41e7 100644 --- a/modules/nf-core/gsea/gsea/environment.yml +++ b/modules/nf-core/gsea/gsea/environment.yml @@ -1,3 +1,4 @@ +name: gsea_gsea channels: - conda-forge - bioconda diff --git a/modules/nf-core/gsea/gsea/main.nf b/modules/nf-core/gsea/gsea/main.nf index 17f4a2e8..6a060c46 100644 --- a/modules/nf-core/gsea/gsea/main.nf +++ b/modules/nf-core/gsea/gsea/main.nf @@ -2,7 +2,7 @@ process GSEA_GSEA { tag "$meta.id" label 'process_single' - conda 'modules/nf-core/gsea/gsea/environment.yml' + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gsea:4.3.2--hdfd78af_0': 'biocontainers/gsea:4.3.2--hdfd78af_0' }" @@ -22,11 +22,11 @@ process GSEA_GSEA { tuple val(meta), path("*gsea_report_for_${target}.html") , emit: report_htmls_target tuple val(meta), path("*ranked_gene_list*.tsv") , emit: ranked_gene_list tuple val(meta), path("*gene_set_sizes.tsv") , emit: gene_set_sizes - tuple val(meta), path("*butterfly_plot.png") , emit: butterfly_plot tuple val(meta), path("*global_es_histogram.png") , emit: histogram tuple val(meta), path("*heat_map_1.png") , emit: heatmap tuple val(meta), path("*pvalues_vs_nes_plot.png") , emit: pvalues_vs_nes_plot tuple val(meta), path("*ranked_list_corr_2.png") , emit: ranked_list_corr + tuple val(meta), path("*butterfly_plot.png") , emit: butterfly_plot, optional: true tuple val(meta), path("*[!gene_set_size|gsea_report|ranked_gene_list]*.tsv"), emit: gene_set_tsv, optional: true tuple val(meta), path("*[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html"), emit: gene_set_html, optional: true tuple val(meta), path("*[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png"), emit: gene_set_heatmap, optional: true diff --git a/modules/nf-core/gsea/gsea/meta.yml b/modules/nf-core/gsea/gsea/meta.yml index 0ff81518..fe2d4c95 100644 --- a/modules/nf-core/gsea/gsea/meta.yml +++ b/modules/nf-core/gsea/gsea/meta.yml @@ -11,7 +11,7 @@ tools: homepage: "http://www.gsea-msigdb.org/gsea/index.jsp" documentation: "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page" doi: "10.1073/pnas.0506580102" - licence: "['BSD-3-clause']" + licence: ["BSD-3-clause"] input: - meta: type: map