From ded3318a0a951ef349ac6785a53c43afef124e79 Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 22 Jun 2023 13:29:43 +0200 Subject: [PATCH 1/6] Added definitions for sizefactors_from_controls and gene_id_col to modules.config/DESeq2 --- conf/modules.config | 2 ++ 1 file changed, 2 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index bdd1ade9..4268494a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -124,9 +124,11 @@ process { ] ] ext.args = { [ + "--gene_id_col \"${params.features_id_col}\"", "--sample_id_col \"${params.observations_id_col}\"", "--test $params.deseq2_test", "--fit_type $params.deseq2_fit_type", + "--sizefactors_from_controls $params.sizefactors_from_controls", "--sf_type $params.deseq2_sf_type", "--min_replicates_for_replace $params.deseq2_min_replicates_for_replace", "--use_t $params.deseq2_use_t", From ac7f408798be24802e06b4e8969bade3a62c15a6 Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 22 Jun 2023 13:44:22 +0200 Subject: [PATCH 2/6] Updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 960f42e5..40be276b 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 - [[#129](https://github.com/nf-core/differentialabundance/pull/129)] - Module updates to fit with recent registry changes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse), [@adamrtalbot](https://github.com/adamrtalbot)) - [[#130](https://github.com/nf-core/differentialabundance/pull/130)] - Document reasons for lack of differential expression ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jfy133](https://github.com/jfy133)) - [[#131](https://github.com/nf-core/differentialabundance/pull/131)] - Improve gtf to table configurability ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) +- [[#137](https://github.com/nf-core/differentialabundance/pull/137)] - Add `--sizefactors_from_controls` and `--gene_id_col` for DESeq2 module to modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) ### `Fixed` From 6fb1354c64894e94ac09eac9bfd2de194b0de795 Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 27 Jun 2023 10:04:33 +0200 Subject: [PATCH 3/6] hopefully fixed control_features bug, this needs to be tested --- nextflow.config | 2 +- workflows/differentialabundance.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 731494e9..a1f604ab 100644 --- a/nextflow.config +++ b/nextflow.config @@ -17,7 +17,7 @@ params { contrasts = null matrix = null control_features = null - sizefactors_from_controls = null + sizefactors_from_controls = false // Reporting logo_file = "${projectDir}/docs/images/nf-core-differentialabundance_logo_light.png" diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf index 198f2a71..d6ffc582 100644 --- a/workflows/differentialabundance.nf +++ b/workflows/differentialabundance.nf @@ -35,7 +35,7 @@ if (params.study_type == 'affy_array'){ } // Check optional parameters -if (params.control_features) { ch_control_features = file(params.control_features, checkIfExists: true) } else { ch_control_features = [[],[]] } +if (params.control_features) { ch_control_features = Channel.of([ exp_meta, file(params.control_features, checkIfExists: true)]) } else { ch_control_features = [[],[]] } if (params.gsea_run) { if (params.gsea_gene_sets){ gene_sets_files = params.gsea_gene_sets.split(",") From a130d5d56f0f099c95240b30a6eb0d153362387b Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 28 Jun 2023 10:34:49 +0200 Subject: [PATCH 4/6] fixed control_features bug with deseq2 --- workflows/differentialabundance.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/differentialabundance.nf b/workflows/differentialabundance.nf index d6ffc582..625b8f30 100644 --- a/workflows/differentialabundance.nf +++ b/workflows/differentialabundance.nf @@ -35,7 +35,7 @@ if (params.study_type == 'affy_array'){ } // Check optional parameters -if (params.control_features) { ch_control_features = Channel.of([ exp_meta, file(params.control_features, checkIfExists: true)]) } else { ch_control_features = [[],[]] } +if (params.control_features) { ch_control_features = Channel.of([ exp_meta, file(params.control_features, checkIfExists: true)]).first() } else { ch_control_features = [[],[]] } if (params.gsea_run) { if (params.gsea_gene_sets){ gene_sets_files = params.gsea_gene_sets.split(",") From 13c372c7491c79a86dc517c0c895bc28786fa2ed Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 28 Jun 2023 13:31:53 +0200 Subject: [PATCH 5/6] updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 40be276b..63644e0d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#116](https://github.com/nf-core/differentialabundance/issues/116)] - Skip outlier detection with low replication ([@pinin4fjords](https://github.com/pinin4fjords), review by [@nvnieuwk](https://github.com/nvnieuwk)) - [[#122](https://github.com/nf-core/differentialabundance/pull/126)] - Add spaces to satisfy nf-core download for singularity ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) - [[#127](https://github.com/nf-core/differentialabundance/issues/127)] - [Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv ([@ctuni](https://github.com/ctuni), review by [@pinin4fjords](https://github.com/pinin4fjords)) +- [[#144](https://github.com/nf-core/differentialabundance/pull/144)] - Fix bugs with --control_features and --sizefactors_from_controls (see issue #138) ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) ## v1.2.0 - 2023-04-19 From 2b30550161d3d4102c5c304d506cdf99259e8cfa Mon Sep 17 00:00:00 2001 From: WackerO <43847497+WackerO@users.noreply.github.com> Date: Wed, 28 Jun 2023 14:18:04 +0200 Subject: [PATCH 6/6] Update CHANGELOG.md Co-authored-by: Jonathan Manning --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 63644e0d..91de6e28 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#116](https://github.com/nf-core/differentialabundance/issues/116)] - Skip outlier detection with low replication ([@pinin4fjords](https://github.com/pinin4fjords), review by [@nvnieuwk](https://github.com/nvnieuwk)) - [[#122](https://github.com/nf-core/differentialabundance/pull/126)] - Add spaces to satisfy nf-core download for singularity ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO)) - [[#127](https://github.com/nf-core/differentialabundance/issues/127)] - [Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv ([@ctuni](https://github.com/ctuni), review by [@pinin4fjords](https://github.com/pinin4fjords)) -- [[#144](https://github.com/nf-core/differentialabundance/pull/144)] - Fix bugs with --control_features and --sizefactors_from_controls (see issue #138) ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) +- [[#138 ](https://github.com/nf-core/differentialabundance/issues/138)]- Fix bugs with --control_features and --sizefactors_from_controls ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords)) ## v1.2.0 - 2023-04-19