From 7fae238d3b34707e8cf818745a949c7bdbd1b237 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 14 Dec 2023 09:38:27 +0100 Subject: [PATCH 1/3] Bump version to 1.4.0 Ran `nf-core bump-version 1.4.0` --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- tests/pipeline/bases2fastq.nf.test.snap | 4 ++-- tests/pipeline/bcl2fastq.nf.test.snap | 4 ++-- tests/pipeline/bclconvert.nf.test.snap | 4 ++-- tests/pipeline/fqtk.nf.test.snap | 4 ++-- tests/pipeline/sgdemux.nf.test.snap | 4 ++-- tests/pipeline/skip_tools.nf.test.snap | 12 ++++++------ 8 files changed, 19 insertions(+), 19 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 6977daec..2ec4cab7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/demultiplex + This report has been generated by the nf-core/demultiplex analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-demultiplex-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index cff0d2e8..4282cf3f 100755 --- a/nextflow.config +++ b/nextflow.config @@ -240,7 +240,7 @@ manifest { description = """Demultiplexing pipeline for Illumina sequencing data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.4.0dev' + version = '1.4.0' doi = '10.5281/zenodo.7153103' } diff --git a/tests/pipeline/bases2fastq.nf.test.snap b/tests/pipeline/bases2fastq.nf.test.snap index 08f262a8..2fc953bf 100644 --- a/tests/pipeline/bases2fastq.nf.test.snap +++ b/tests/pipeline/bases2fastq.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions": { "content": [ - "{BASES2FASTQ={bases2fastq=1.1.0.593880262, use subject to license available at elementbiosciences.com}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BASES2FASTQ={bases2fastq=1.1.0.593880262, use subject to license available at elementbiosciences.com}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T16:57:34.674489" }, @@ -15,4 +15,4 @@ ], "timestamp": "2023-12-11T16:40:05.942646" } -} \ No newline at end of file +} diff --git a/tests/pipeline/bcl2fastq.nf.test.snap b/tests/pipeline/bcl2fastq.nf.test.snap index e6d68979..2e540a84 100644 --- a/tests/pipeline/bcl2fastq.nf.test.snap +++ b/tests/pipeline/bcl2fastq.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions": { "content": [ - "{BCL2FASTQ={bcl2fastq=2.20.0.422}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCL2FASTQ={bcl2fastq=2.20.0.422}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T16:55:21.645426" }, @@ -70,4 +70,4 @@ ], "timestamp": "2023-12-11T16:55:21.680453" } -} \ No newline at end of file +} diff --git a/tests/pipeline/bclconvert.nf.test.snap b/tests/pipeline/bclconvert.nf.test.snap index 5fdda8b7..b9f9f952 100644 --- a/tests/pipeline/bclconvert.nf.test.snap +++ b/tests/pipeline/bclconvert.nf.test.snap @@ -24,7 +24,7 @@ }, "software_versions": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T16:56:35.649441" }, @@ -36,4 +36,4 @@ ], "timestamp": "2023-12-11T16:56:35.661017" } -} \ No newline at end of file +} diff --git a/tests/pipeline/fqtk.nf.test.snap b/tests/pipeline/fqtk.nf.test.snap index a483e0c8..3de14c5a 100644 --- a/tests/pipeline/fqtk.nf.test.snap +++ b/tests/pipeline/fqtk.nf.test.snap @@ -7,8 +7,8 @@ }, "software_versions": { "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, FQTK={fqtk=0.2.1}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, FQTK={fqtk=0.2.1}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T17:05:36.315291" } -} \ No newline at end of file +} diff --git a/tests/pipeline/sgdemux.nf.test.snap b/tests/pipeline/sgdemux.nf.test.snap index 0a68ffc5..8ca7d4de 100644 --- a/tests/pipeline/sgdemux.nf.test.snap +++ b/tests/pipeline/sgdemux.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions": { "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, SGDEMUX={sgdemux=1.1.1}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, SGDEMUX={sgdemux=1.1.1}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T16:59:13.85618" }, @@ -14,4 +14,4 @@ ], "timestamp": "2023-10-17T08:01:14+0000" } -} \ No newline at end of file +} diff --git a/tests/pipeline/skip_tools.nf.test.snap b/tests/pipeline/skip_tools.nf.test.snap index 00b82028..d9bea04c 100644 --- a/tests/pipeline/skip_tools.nf.test.snap +++ b/tests/pipeline/skip_tools.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions_skip_trimming": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T17:00:30.102965" }, @@ -95,25 +95,25 @@ }, "software_versions_skip_fastqc": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T17:02:16.631766" }, "software_versions_skip_fastp_fastqc": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T17:02:44.134341" }, "software_versions_skip_multiqc": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T17:03:50.096961" }, "software_versions_skip_fastp": { "content": [ - "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0dev}}" + "{BCLCONVERT={bclconvert=00.000.000.4.2.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, Workflow={nf-core/demultiplex=1.4.0}}" ], "timestamp": "2023-12-11T17:00:57.483981" }, @@ -139,4 +139,4 @@ ], "timestamp": "2023-12-11T16:43:15.513271" } -} \ No newline at end of file +} From ee7fe5d929da9fc361df09ce3c7547752b02492e Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 14 Dec 2023 09:54:48 +0100 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a004f55c..5934d01a 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unpublished Version / DEV] +## 1.4.0 - 2023-12-14 + ### `Added` - [#148](https://github.com/nf-core/demultiplex/pull/148) Update CODEOWNERS to use GitHub teams @@ -25,7 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## `Removed` -- Remove `public_aws_ecr` profile. +- [#130](https://github.com/nf-core/demultiplex/pull/130) Remove `public_aws_ecr` profile. ## 1.3.2 - 2023-06-07 From 1588ebbbe3a16a2370e7e5ab1bffc7da1160a0c4 Mon Sep 17 00:00:00 2001 From: Adrien Coulier Date: Thu, 14 Dec 2023 12:05:58 +0100 Subject: [PATCH 3/3] Fix indentation nextflow.config Co-authored-by: Maxime U Garcia --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 4282cf3f..ceaf4ea6 100755 --- a/nextflow.config +++ b/nextflow.config @@ -240,7 +240,7 @@ manifest { description = """Demultiplexing pipeline for Illumina sequencing data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.4.0' + version = '1.4.0' doi = '10.5281/zenodo.7153103' }