From 7533e9f48da38f303bb7f65b4d74cd182bf918b0 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 20 Nov 2023 14:43:01 +0000 Subject: [PATCH 01/10] Ensure pseudoaligner is set if pseudoalignment is not skipped --- nextflow.config | 2 +- workflows/rnaseq.nf | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index d42914210..6a5788e2f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -58,7 +58,7 @@ params { // Alignment aligner = 'star_salmon' - pseudo_aligner = null + pseudo_aligner = 'salmon' seq_center = null bam_csi_index = false star_ignore_sjdbgtf = false diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index 403194ac2..4547162a9 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -37,7 +37,13 @@ if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list) def prepareToolIndices = [] if (!params.skip_bbsplit) { prepareToolIndices << 'bbsplit' } if (!params.skip_alignment) { prepareToolIndices << params.aligner } -if (!params.skip_pseudo_alignment && params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner } +if (!params.skip_pseudo_alignment) { + if(params.pseudo_aligner) { + prepareToolIndices << params.pseudo_aligner + } else { + exit 1, "--skip_pseudo_alignment not set, but --pseudo_aligner not set" + } +} // Determine whether to filter the GTF or not def filterGtf = From 10d808666bc4b08a2912828cdc2e107e1726b342 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 20 Nov 2023 14:51:40 +0000 Subject: [PATCH 02/10] Update changelog --- CHANGELOG.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4680c417a..c6687990b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,11 +3,17 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-20 + +### Enhancements & fixes + +- [PR #1124](https://github.com/nf-core/rnaseq/pull/1124) - Ensure pseudoaligner is set if pseudoalignment is not skipped + ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17 ### Enhancements and fixes -- [[PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix +- [PR #1121](https://github.com/nf-core/rnaseq/pull/1121) - Changes for 3.13.1 patch release incl. igenomes star fix ## [[3.13.0](https://github.com/nf-core/rnaseq/releases/tag/3.13.0)] - 2023-11-17 From 279fd121ae0264282aa0bde0826b37e64de131de Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 20 Nov 2023 16:21:48 +0000 Subject: [PATCH 03/10] [skip ci] bump version in config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 6a5788e2f..41bcb45d3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -317,7 +317,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.13.1' + version = '3.13.2' doi = 'https://doi.org/10.5281/zenodo.1400710' } From 8ed06f36c9702d82dd6979086caa64d44c61f0d2 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 20 Nov 2023 16:51:43 +0000 Subject: [PATCH 04/10] Move release to minor version, include tximport PR --- CHANGELOG.md | 3 ++- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c6687990b..7f713bf2d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,10 +3,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-20 +## [[3.14.0](https://github.com/nf-core/rnaseq/releases/tag/3.14.0)] - 2023-11-21 ### Enhancements & fixes +- [PR #1123](https://github.com/nf-core/rnaseq/pull/1123) - Overhaul tximport.r, output length tables - [PR #1124](https://github.com/nf-core/rnaseq/pull/1124) - Ensure pseudoaligner is set if pseudoalignment is not skipped ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17 diff --git a/nextflow.config b/nextflow.config index 41bcb45d3..933f48cf4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -317,7 +317,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.13.2' + version = '3.14.0' doi = 'https://doi.org/10.5281/zenodo.1400710' } From 8615a86bcd49c097c2b2cc680742a38d12019fe5 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 20 Nov 2023 17:38:26 +0000 Subject: [PATCH 05/10] [skip ci] Back to patch release --- CHANGELOG.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7f713bf2d..7b85720a5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [[3.14.0](https://github.com/nf-core/rnaseq/releases/tag/3.14.0)] - 2023-11-21 +## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21 ### Enhancements & fixes diff --git a/nextflow.config b/nextflow.config index 933f48cf4..41bcb45d3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -317,7 +317,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.14.0' + version = '3.13.2' doi = 'https://doi.org/10.5281/zenodo.1400710' } From 0a675cf585906c152c8c44514188ff24644a9a17 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 20 Nov 2023 18:53:29 +0000 Subject: [PATCH 06/10] Fix error message --- bin/filter_gtf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/filter_gtf.py b/bin/filter_gtf.py index 265250627..b4a662cad 100755 --- a/bin/filter_gtf.py +++ b/bin/filter_gtf.py @@ -30,7 +30,7 @@ def tab_delimited(file: str) -> float: def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None: """Filter GTF file based on FASTA sequence names.""" if tab_delimited(gtf_in) != 8: - raise ValueError("Invalid GTF file: Expected 8 tab-separated columns.") + raise ValueError("Invalid GTF file: Expected 9 tab-separated columns.") seq_names_in_genome = extract_fasta_seq_names(fasta) logger.info(f"Extracted chromosome sequence names from {fasta}") From e1a5cca1a80bd170f3ec01e543002bcff7786cbf Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 20 Nov 2023 19:12:22 +0000 Subject: [PATCH 07/10] [automated] Fix linting with Prettier --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index de0d10fec..91063f2fd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - ## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21 ### Enhancements & fixes From 89666a475d02a8dd68ab1cc5d681bbd84d59f9b1 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 20 Nov 2023 19:16:22 +0000 Subject: [PATCH 08/10] Add credits --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 91063f2fd..ac5484688 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21 +### Credits + +Special thanks to the following for their contributions to the release: + +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Regina Hertfelder Reynolds](https://github.com/RHReynolds) +- [Matthias Zepper](https://github.com/MatthiasZepper) + ### Enhancements & fixes - [PR #1123](https://github.com/nf-core/rnaseq/pull/1123) - Overhaul tximport.r, output length tables From 36c420413355109517e47ca2a5e1fed619de112e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 21 Nov 2023 10:39:37 +0100 Subject: [PATCH 09/10] [skipci] Update CHANGELOG.md --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4ee05f00e..6ef0b84d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,8 +17,8 @@ Special thanks to the following for their contributions to the release: - [PR #1123](https://github.com/nf-core/rnaseq/pull/1123) - Overhaul tximport.r, output length tables - [PR #1124](https://github.com/nf-core/rnaseq/pull/1124) - Ensure pseudoaligner is set if pseudoalignment is not skipped -- [[PR #1126](https://github.com/nf-core/rnaseq/pull/1126)] [[#1125](https://github.com/nf-core/rnaseq/issues/1125)] - Pipeline fails if transcript_fasta not provided and `skip_gtf_filter = true`. -- [[PR #1127](https://github.com/nf-core/rnaseq/pull/1127)] - Enlarge sampling to determine the number of columns in `filter_gtf.py` script. +- [PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Pipeline fails if transcript_fasta not provided and `skip_gtf_filter = true`. +- [PR #1127](https://github.com/nf-core/rnaseq/pull/1127) - Enlarge sampling to determine the number of columns in `filter_gtf.py` script. ## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17 From cfd9270b6e42a27e3175b1635ec9233d74652e07 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 21 Nov 2023 10:15:52 +0000 Subject: [PATCH 10/10] Always check --skip_pseudo_alignment and --pseudo_aligner are set --- conf/modules.config | 3 +-- nextflow.config | 2 +- workflows/rnaseq.nf | 13 +++---------- 3 files changed, 5 insertions(+), 13 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 6e28f549b..efef36974 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1087,7 +1087,6 @@ if (!params.skip_multiqc) { if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') { process { - withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT' { ext.args = { params.extra_salmon_quant_args ?: '' } publishDir = [ @@ -1112,7 +1111,7 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') { } } -if (!params.skip_pseudo_alignment) { +if (!params.skip_pseudo_alignment && params.pseudo_aligner) { process { withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE' { publishDir = [ diff --git a/nextflow.config b/nextflow.config index 41bcb45d3..89f72ec5b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -58,7 +58,7 @@ params { // Alignment aligner = 'star_salmon' - pseudo_aligner = 'salmon' + pseudo_aligner = null seq_center = null bam_csi_index = false star_ignore_sjdbgtf = false diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index 4547162a9..f8def2d10 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -37,13 +37,7 @@ if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list) def prepareToolIndices = [] if (!params.skip_bbsplit) { prepareToolIndices << 'bbsplit' } if (!params.skip_alignment) { prepareToolIndices << params.aligner } -if (!params.skip_pseudo_alignment) { - if(params.pseudo_aligner) { - prepareToolIndices << params.pseudo_aligner - } else { - exit 1, "--skip_pseudo_alignment not set, but --pseudo_aligner not set" - } -} +if (!params.skip_pseudo_alignment && params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner } // Determine whether to filter the GTF or not def filterGtf = @@ -822,9 +816,8 @@ workflow RNASEQ { // ch_pseudo_multiqc = Channel.empty() ch_pseudoaligner_pca_multiqc = Channel.empty() - ch_pseudoaligner_clustering_multiqc = Channel.empty() - - if (!params.skip_pseudo_alignment) { + ch_pseudoaligner_clustering_multiqc = Channel.empty() + if (!params.skip_pseudo_alignment && params.pseudo_aligner) { if (params.pseudo_aligner == 'salmon') { ch_pseudo_index = PREPARE_GENOME.out.salmon_index