From c0c63478ef4628f6abfb85c294dcd533044eca6b Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 3 Jul 2024 10:43:03 +0200 Subject: [PATCH 1/4] Fix changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1d0102de..b5630f67 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10). - [[#367](https://github.com/nf-core/chipseq/issues/367)] - Get rid of `CheckIfExists` for params paths. - [[#370](https://github.com/nf-core/chipseq/issues/370)] - Fix stack overflow exceptions in phantompeakqualtools ([see here](https://github.com/kundajelab/phantompeakqualtools/issues/3)). -- [[PR #391](https://github.com/nf-core/chipseq/pull/391)] - Get rid of the `lib` folder and rearrange the pipeline accordingly. +- [[#387](https://github.com/nf-core/chipseq/issues/387)] - Get rid of the `lib` folder and rearrange the pipeline accordingly. ### Software dependencies From a628cc467441419aeabb56514c2505b5e8d723a3 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 3 Jul 2024 10:43:40 +0200 Subject: [PATCH 2/4] Fix save_unaligned parameter description in schema --- CHANGELOG.md | 1 + nextflow_schema.json | 12 +++++++++++- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b5630f67..5677e847 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#367](https://github.com/nf-core/chipseq/issues/367)] - Get rid of `CheckIfExists` for params paths. - [[#370](https://github.com/nf-core/chipseq/issues/370)] - Fix stack overflow exceptions in phantompeakqualtools ([see here](https://github.com/kundajelab/phantompeakqualtools/issues/3)). - [[#387](https://github.com/nf-core/chipseq/issues/387)] - Get rid of the `lib` folder and rearrange the pipeline accordingly. +- [[#385](https://github.com/nf-core/chipseq/issues/385)] - Fix `--save_unaligned` description in schema. ### Software dependencies diff --git a/nextflow_schema.json b/nextflow_schema.json index 668e4c4d..b0e6317c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -261,7 +261,7 @@ "save_unaligned": { "type": "boolean", "fa_icon": "fas fa-save", - "description": "Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.", + "description": "Save unaligned sequences to the output directory (only available for Bowtie 2 And STAR.", "help_text": "This may either be in the form of FastQ or BAM files depending on the options available for that particular tool." }, "bamtools_filter_pe_config": { @@ -399,6 +399,16 @@ "description": "Skip MultiQC.", "fa_icon": "fas fa-fast-forward" }, + "skip_peak_calling": { + "type": "boolean", + "description": "Skip MACS2 peak calling.", + "fa_icon": "fas fa-fast-forward" + }, + "skip_reporting": { + "type": "boolean", + "description": "Skip reporting.", + "fa_icon": "fas fa-fast-forward" + }, "skip_qc": { "type": "boolean", "fa_icon": "fas fa-fast-forward", From f6b9c2707ba4b4ac677034e862c078fa20674d9e Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 3 Jul 2024 11:16:17 +0200 Subject: [PATCH 3/4] Remove code leak --- nextflow_schema.json | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index b0e6317c..b7c4e106 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -399,16 +399,6 @@ "description": "Skip MultiQC.", "fa_icon": "fas fa-fast-forward" }, - "skip_peak_calling": { - "type": "boolean", - "description": "Skip MACS2 peak calling.", - "fa_icon": "fas fa-fast-forward" - }, - "skip_reporting": { - "type": "boolean", - "description": "Skip reporting.", - "fa_icon": "fas fa-fast-forward" - }, "skip_qc": { "type": "boolean", "fa_icon": "fas fa-fast-forward", From ac7feeec2c4fd02fc3c830019808486c1cbe2da8 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Wed, 3 Jul 2024 11:28:38 +0200 Subject: [PATCH 4/4] Update nextflow_schema.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index b7c4e106..f51e0940 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -261,7 +261,7 @@ "save_unaligned": { "type": "boolean", "fa_icon": "fas fa-save", - "description": "Save unaligned sequences to the output directory (only available for Bowtie 2 And STAR.", + "description": "Save unaligned sequences to the output directory (only available for Bowtie 2 and STAR.", "help_text": "This may either be in the form of FastQ or BAM files depending on the options available for that particular tool." }, "bamtools_filter_pe_config": {