From 6fb1354c64894e94ac09eac9bfd2de194b0de795 Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 27 Jun 2023 10:04:33 +0200 Subject: [PATCH 1/4] 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 2/4] 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 3/4] 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 4/4] 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