From f95237400cc263d5e531cbd039e84e39d1999ea4 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Mon, 20 Mar 2023 09:12:22 +0100 Subject: [PATCH 01/10] bump version to 2.3.0dev --- CHANGELOG.md | 2 ++ nextflow.config | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 06336809..05687d88 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,8 @@ 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). +## v2.3.0dev + ## v2.2.0 - Added support to output 10x count files in text format. diff --git a/nextflow.config b/nextflow.config index bedb5bda..c165a3fc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -225,7 +225,7 @@ manifest { description = """Pipeline for processing 10x Genomics single cell rnaseq data""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.2.0' + version = '2.3.0dev' doi = '10.5281/zenodo.3568187' } From 34a2b6ca00c7febe020ef1d8dd477534de2476c4 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 28 Mar 2023 12:57:48 +0000 Subject: [PATCH 02/10] fixing ifelse checking minimum number of columns --- bin/check_samplesheet.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 6fd8067c..3283c11e 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -104,7 +104,8 @@ def check_samplesheet(file_in, file_out): min_header_count = min_header_count + 1 colmap[h] = i i = i + 1 - if unknown_header or min_header_count < len(MIN_HEADER): + if min_header_count < len(MIN_HEADER): + # code was checking for unknown_header or min_header_count however looking at the ifelse, unknown_header does not seem that it should be tested given = ",".join(header) wanted = ",".join(MIN_HEADER) print(f"ERROR: Please check samplesheet header -> {given} != {wanted}") From e91d75028817a2afb9256ecbea0fb4f3cd257345 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 28 Mar 2023 13:02:45 +0000 Subject: [PATCH 03/10] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 05687d88..3c64cc34 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v2.3.0dev +- Fix problem on samplesheet check related to amount of columns ([[#211](https://github.com/nf-core/scrnaseq/issues/211)]) + ## v2.2.0 - Added support to output 10x count files in text format. From 4f66ce82d2fa41f677a373d2895eb21be18a0ea9 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 20 Apr 2023 12:36:46 +0000 Subject: [PATCH 04/10] Fix bugs where sensible defaults haven't been set for params --- nextflow.config | 4 ++-- nextflow_schema.json | 8 ++++---- workflows/scrnaseq.nf | 4 +--- 3 files changed, 7 insertions(+), 9 deletions(-) diff --git a/nextflow.config b/nextflow.config index c165a3fc..7bc1949a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -43,11 +43,11 @@ params { cellranger_index = null // UniverSC paramaters - universc_index = null + universc_index = null universc_technology = '10x' // Template Boilerplate options - skip_multiqc = false + skip_multiqc = false // References genome = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 30df1ee9..0df6b259 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -182,8 +182,7 @@ }, "seq_center": { "type": "string", - "description": "Name of sequencing center for BAM read group tag.", - "default": "None" + "description": "Name of sequencing center for BAM read group tag." }, "star_feature": { "type": "string", @@ -251,11 +250,12 @@ "properties": { "universc_index": { "type": "string", - "description": "Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website. " + "description": "Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website." }, "universc_technology": { "type": "string", - "description": "Specify a single-cell technology, vendor, or platform. See the UniverSC documentation or GitHub repository for more details. " + "description": "Specify a single-cell technology, vendor, or platform. See the UniverSC documentation or GitHub repository for more details.", + "default": "10x" } } }, diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf index 24cde48a..fbc0259c 100644 --- a/workflows/scrnaseq.nf +++ b/workflows/scrnaseq.nf @@ -104,8 +104,6 @@ ch_cellranger_index = params.cellranger_index ? file(params.cellranger_index) : //universc params ch_universc_index = params.universc_index ? file(params.universc_index) : [] -ch_universc_technology = params.universc_technology - workflow SCRNASEQ { @@ -201,7 +199,7 @@ workflow SCRNASEQ { ch_genome_fasta, ch_filter_gtf, ch_universc_index, - ch_universc_technology, + params.universc_technology, ch_fastq ) ch_versions = ch_versions.mix(UNIVERSC_ALIGN.out.ch_versions) From 5e15b65c7107bfe5198a253dbb0700fed1d47fb4 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 20 Apr 2023 12:40:17 +0000 Subject: [PATCH 05/10] Remove unused --bustools_correct and --skip_bustools --- nextflow.config | 2 -- nextflow_schema.json | 10 ---------- 2 files changed, 12 deletions(-) diff --git a/nextflow.config b/nextflow.config index 7bc1949a..0bf90372 100644 --- a/nextflow.config +++ b/nextflow.config @@ -11,7 +11,6 @@ params { // generic options aligner = 'alevin' - bustools_correct = true outdir = null input = null save_reference = false @@ -30,7 +29,6 @@ params { // kallist bustools parameters kallisto_gene_map = null kallisto_index = null - skip_bustools = false kb_workflow = "standard" // STARsolo parameters diff --git a/nextflow_schema.json b/nextflow_schema.json index 0df6b259..2061e7c0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -206,16 +206,6 @@ "description": "Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.", "fa_icon": "fas fa-fish" }, - "bustools_correct": { - "type": "boolean", - "description": "If set to false, skip the correct steps after mapping with Kallisto.", - "fa_icon": "fas fa-bus-alt" - }, - "skip_bustools": { - "type": "boolean", - "description": "Skip BUStools entirely in workflow", - "fa_icon": "fas fa-forward" - }, "kallisto_index": { "type": "string", "description": "Specify a path to the precomputed Kallisto index.", From 2eec000ca7055f4ae7428983c9a73281235990ac Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Thu, 27 Apr 2023 18:22:15 +0000 Subject: [PATCH 06/10] Ensure that starsolo outputs channel that matches others, including meta map. --- subworkflows/local/starsolo.nf | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf index cf771999..6d598fb8 100644 --- a/subworkflows/local/starsolo.nf +++ b/subworkflows/local/starsolo.nf @@ -56,7 +56,5 @@ workflow STARSOLO { star_index = star_index star_result = STAR_ALIGN.out.tab star_counts = STAR_ALIGN.out.counts - for_multiqc = STAR_ALIGN.out.log_final.collect{it[1]}.ifEmpty([]) - - + for_multiqc = STAR_ALIGN.out.log_final } From c3f9370c620d2f797feff2e67838e53fe98cce8e Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Fri, 28 Apr 2023 11:43:17 -0400 Subject: [PATCH 07/10] Remove trailing commas from the MultiQC inputs --- workflows/scrnaseq.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf index fbc0259c..3c607c5e 100644 --- a/workflows/scrnaseq.nf +++ b/workflows/scrnaseq.nf @@ -236,8 +236,8 @@ workflow SCRNASEQ { ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_fastqc.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_alevin.collect{it[1]}.ifEmpty([])), - ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_star.collect{it[1]}.ifEmpty([])), + ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_alevin.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_star.collect{it[1]}.ifEmpty([])) MULTIQC ( ch_multiqc_files.collect(), From 92768e6c74450dc896f1f7342be6ca27efdbe6ef Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Fri, 28 Apr 2023 12:40:01 -0400 Subject: [PATCH 08/10] Changelog update --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c64cc34..d00b4c71 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,8 +4,8 @@ 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). ## v2.3.0dev - - Fix problem on samplesheet check related to amount of columns ([[#211](https://github.com/nf-core/scrnaseq/issues/211)]) +- Fixed bug in starsolo output cardinality. ## v2.2.0 From 4f393da70b69960d0b012cebfd8d30fc6405a07b Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Fri, 28 Apr 2023 13:37:40 -0400 Subject: [PATCH 09/10] Prettier fix --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d00b4c71..270d709e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,7 @@ 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). ## v2.3.0dev + - Fix problem on samplesheet check related to amount of columns ([[#211](https://github.com/nf-core/scrnaseq/issues/211)]) - Fixed bug in starsolo output cardinality. From 81120b01ec7f3b821c414273d3a5ad6252508d56 Mon Sep 17 00:00:00 2001 From: Rob Syme Date: Tue, 2 May 2023 13:07:03 -0400 Subject: [PATCH 10/10] Readying for 2.3.0 release --- CHANGELOG.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 270d709e..603229e5 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). -## v2.3.0dev +## v2.3.0 Steelblue Waspaloy Dachshund - Fix problem on samplesheet check related to amount of columns ([[#211](https://github.com/nf-core/scrnaseq/issues/211)]) - Fixed bug in starsolo output cardinality. diff --git a/nextflow.config b/nextflow.config index 0bf90372..c2977bd7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -223,7 +223,7 @@ manifest { description = """Pipeline for processing 10x Genomics single cell rnaseq data""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.3.0dev' + version = '2.3.0' doi = '10.5281/zenodo.3568187' }