From d6051c35818101aa9b811ba6a19e2810154d5753 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 1 Apr 2023 10:36:06 +0100 Subject: [PATCH 1/7] Bump pipeline version to 3.12.0dev --- CHANGELOG.md | 4 ++++ nextflow.config | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2d5191059..48dd5ce15 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ 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). +## [Unpublished Version / DEV] + +### Enhancements & fixes + ## [[3.11.1](https://github.com/nf-core/rnaseq/releases/tag/3.11.1)] - 2023-03-31 ### Credits diff --git a/nextflow.config b/nextflow.config index a5b94fd04..f851618cf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -261,7 +261,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '3.11.1' + version = '3.12.0dev' doi = 'https://doi.org/10.5281/zenodo.1400710' } From a1ac80ce4a02d724ebf1f0b2727a9aa5d024b924 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 21 Apr 2023 18:20:39 +0200 Subject: [PATCH 2/7] Update test.config add default URLs to file as comment --- conf/test.config | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/conf/test.config b/conf/test.config index 57811683c..a4181cf3a 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,18 +20,28 @@ params { max_time = '6.h' // Input data + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/samplesheet/v3.10/samplesheet_test.csv input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv" // Genome references + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/genome.fasta fasta = "${params.test_data_base}/reference/genome.fasta" + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz gtf = "${params.test_data_base}/reference/genes.gtf.gz" + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz gff = "${params.test_data_base}/reference/genes.gff.gz" + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta transcript_fasta = "${params.test_data_base}/reference/transcriptome.fasta" + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz additional_fasta = "${params.test_data_base}/reference/gfp.fa.gz" + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt" + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz hisat2_index = "${params.test_data_base}/reference/hisat2.tar.gz" + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz salmon_index = "${params.test_data_base}/reference/salmon.tar.gz" + // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz rsem_index = "${params.test_data_base}/reference/rsem.tar.gz" // Other parameters From 92dde77070cf7a2ec060e947af1c37d27b76db3e Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Sat, 22 Apr 2023 17:53:10 -0400 Subject: [PATCH 3/7] Ensure that FASTQ_SUBSAMPLE_FQ_SALMON is provided a value channel for genome fastq. Without this fix, we risk indexing the genome for each sample rather than just once for all samples. --- workflows/rnaseq.nf | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index 87630bead..9876e09b1 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -247,6 +247,7 @@ workflow RNASEQ { PREPARE_GENOME.out.fasta .combine(ch_strand_fastq.auto_strand) .map { it.first() } + .first() .set { ch_genome_fasta } FASTQ_SUBSAMPLE_FQ_SALMON ( @@ -321,7 +322,7 @@ workflow RNASEQ { // // Get list of samples that failed trimming threshold for MultiQC report - // + // ch_trim_read_count .map { meta, num_reads -> @@ -332,7 +333,7 @@ workflow RNASEQ { } } .collect() - .map { + .map { tsv_data -> def header = ["Sample", "Reads after trimming"] WorkflowRnaseq.multiqcTsvFromList(tsv_data, header) @@ -604,7 +605,7 @@ workflow RNASEQ { ch_pass_fail_mapped .fail .collect() - .map { + .map { tsv_data -> def header = ["Sample", "STAR uniquely mapped reads (%)"] WorkflowRnaseq.multiqcTsvFromList(tsv_data, header) @@ -765,7 +766,7 @@ workflow RNASEQ { ch_versions = ch_versions.mix(BAM_RSEQC.out.versions) ch_inferexperiment_multiqc - .map { + .map { meta, strand_log -> def inferred_strand = WorkflowRnaseq.getInferexperimentStrandedness(strand_log, 30) pass_strand_check[meta.id] = true @@ -775,7 +776,7 @@ workflow RNASEQ { } } .collect() - .map { + .map { tsv_data -> def header = [ "Sample", From b17524a5af68a1bbd770f20eb4dc799164207f2c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 24 Apr 2023 11:22:52 +0100 Subject: [PATCH 4/7] Update all nf-core/modules --- modules.json | 4 ++-- .../dumpsoftwareversions/templates/dumpsoftwareversions.py | 0 modules/nf-core/qualimap/rnaseq/main.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) mode change 100755 => 100644 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/modules.json b/modules.json index a209ca3d2..fe948649c 100644 --- a/modules.json +++ b/modules.json @@ -17,7 +17,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "b6d4d476aee074311c89d82a69c1921bd70c8180", + "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b", "installed_by": ["modules"] }, "custom/getchromsizes": { @@ -77,7 +77,7 @@ }, "qualimap/rnaseq": { "branch": "master", - "git_sha": "75027bf77472b1f4fd2cdd7e46f83119dfb0f2c6", + "git_sha": "0a9c4eb264cce197707491861ce058a4c79d9c4f", "installed_by": ["modules"] }, "rsem/calculateexpression": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py old mode 100755 new mode 100644 diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index c3cd5c06e..b84ca060b 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -32,7 +32,7 @@ process QUALIMAP_RNASEQ { } """ unset DISPLAY - mkdir tmp + mkdir -p tmp export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp qualimap \\ --java-mem-size=$memory \\ From 156da921f5c41fded6932016823e94894bbad101 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 24 Apr 2023 11:23:07 +0100 Subject: [PATCH 5/7] Define params.test_data_base default once in test.config --- conf/test.config | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/conf/test.config b/conf/test.config index a4181cf3a..7ba43957c 100644 --- a/conf/test.config +++ b/conf/test.config @@ -19,29 +19,21 @@ params { max_memory = '6.GB' max_time = '6.h' + // Input data - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/samplesheet/v3.10/samplesheet_test.csv + // params.test_data_base (default) = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/' input = "${params.test_data_base}/samplesheet/v3.10/samplesheet_test.csv" // Genome references - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/genome.fasta fasta = "${params.test_data_base}/reference/genome.fasta" - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz gtf = "${params.test_data_base}/reference/genes.gtf.gz" - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz gff = "${params.test_data_base}/reference/genes.gff.gz" - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta transcript_fasta = "${params.test_data_base}/reference/transcriptome.fasta" - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz additional_fasta = "${params.test_data_base}/reference/gfp.fa.gz" - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt" - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz hisat2_index = "${params.test_data_base}/reference/hisat2.tar.gz" - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz salmon_index = "${params.test_data_base}/reference/salmon.tar.gz" - // https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz rsem_index = "${params.test_data_base}/reference/rsem.tar.gz" // Other parameters From b4dace1fd501ec6b8e57e56d1b29ef3c47bf629c Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 24 Apr 2023 11:23:37 +0100 Subject: [PATCH 6/7] Bump pipeline version to 3.11.2 --- CHANGELOG.md | 12 +++++++++++- nextflow.config | 2 +- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 48dd5ce15..083795d99 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,10 +3,20 @@ 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). -## [Unpublished Version / DEV] +## [[3.11.2](https://github.com/nf-core/rnaseq/releases/tag/3.11.2)] - 2023-04-25 + +### Credits + +Special thanks to the following for their code contributions to the release: + +- [Maxime Garcia](https://github.com/maxulysse) +- [Rob Syme](https://github.com/robsyme) +- [W. Lee Pang](https://github.com/wleepang) ### Enhancements & fixes +- [[#1003](https://github.com/nf-core/rnaseq/pull/1003)] - `FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX` is launched multiple times and fails + ## [[3.11.1](https://github.com/nf-core/rnaseq/releases/tag/3.11.1)] - 2023-03-31 ### Credits diff --git a/nextflow.config b/nextflow.config index f851618cf..2774ee936 100644 --- a/nextflow.config +++ b/nextflow.config @@ -261,7 +261,7 @@ manifest { description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '3.12.0dev' + version = '3.11.2' doi = 'https://doi.org/10.5281/zenodo.1400710' } From 7f61509634fad6500c3e52068a2d3bf723c728c2 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Mon, 24 Apr 2023 23:08:33 +0100 Subject: [PATCH 7/7] Update CHANGELOG.md --- CHANGELOG.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 083795d99..71db55899 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,12 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Credits -Special thanks to the following for their code contributions to the release: +Special thanks to the following for their contributions to the release: +- [Jonathan Manning](https://github.com/pinin4fjords) - [Maxime Garcia](https://github.com/maxulysse) - [Rob Syme](https://github.com/robsyme) - [W. Lee Pang](https://github.com/wleepang) +Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. + ### Enhancements & fixes - [[#1003](https://github.com/nf-core/rnaseq/pull/1003)] - `FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX` is launched multiple times and fails