v1.1.0 #23
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v1.1.0 #23
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Important! Template update for nf-core/tools v3.0.2
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mashehu
reviewed
Dec 2, 2024
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@matq007 Do you need some help to finalize this release? :) |
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I just need a PR review, the pipeline is works locally ^_^ |
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But there are three tests which are marked as required and are not running? |
famosab
reviewed
Mar 12, 2025
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Left a couple of questions. My main thing would be:
Try to do changes that go into the changelog in small PRs (like anew subworkflow) - these are easily reviewable. To me it seems that many commits went into this release PR but these were not reviewed in th emeantime (?).
And use nf-core pipelines bump-version to update to a version for the release. I would also suggest to include the release name in the changelog. https://www.codenamegenerator.com/ can be used for name finding :)
| org: nf-core | ||
| outdir: . | ||
| skip_features: null | ||
| version: 1.0.3 |
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If this is for a new release this needs to be bumped up, I guess to 1.1.0?
| @@ -3,6 +3,40 @@ | |||
| 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). | |||
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| ## [unreleased] | |||
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If this is for a release this needs to be updated to
v1.1.0 - [date] - release name?
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| - linting issues - ([bedc4a8](https://github.com/nf-core/marsseq/commit/bedc4a887ed804a0f2a5168a4f59090b083d40bd)) | ||
| - test config - ([0b9410b](https://github.com/nf-core/marsseq/commit/0b9410bcb19ac0e3630ebd500e5891851e0c2c2b)) | ||
| - check that provided xlsx files are not empty after subset - ([e88075b](https://github.com/nf-core/marsseq/commit/e88075be0f56d9791229bfe590dba594a10122ce)) | ||
| - missing openpyxl in conda specification - ([41d617b](https://github.com/nf-core/marsseq/commit/41d617b3aa0deece111487ea29d208489662948c)) | ||
| - missing openpyxl conda dependency - ([d47f7f0](https://github.com/nf-core/marsseq/commit/d47f7f02a9b3367d870bd9b460df6811b61e95aa)) | ||
| - replace ubuntu image with conda packages - ([b4ef5a5](https://github.com/nf-core/marsseq/commit/b4ef5a520ff401a75451242df34e02aebccd3068)) | ||
| - perl not anymore in bioconda channel - ([7c8cf13](https://github.com/nf-core/marsseq/commit/7c8cf1320f0ff01710f48d1f08000c71351f1ab1)) | ||
| - move uncompressed genome and annotation to reference folder - ([4dea965](https://github.com/nf-core/marsseq/commit/4dea96557937785970ca12755a212817113e0753)) | ||
| - small and full AWS test - ([b72d716](https://github.com/nf-core/marsseq/commit/b72d716416f2c37499c708f2f9f4d1e415e0dfd5)) | ||
| - linting - ([4f6feee](https://github.com/nf-core/marsseq/commit/4f6feeefe85bfd5547bef81b38e052f6cf2f79e1)) | ||
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| ### Documentation | ||
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| - linting for CITATIONS - ([98b5159](https://github.com/nf-core/marsseq/commit/98b5159c997ad964166c95de01c0673adc964695)) | ||
| - updated CHANGELOG - ([5a4e7f2](https://github.com/nf-core/marsseq/commit/5a4e7f2cdd5757cd1094a5534cddd702c173449e)) | ||
| - updated workflow and outputs - ([cddbe3b](https://github.com/nf-core/marsseq/commit/cddbe3b44b7fd0aa189b78eb3f79379ba74091b0)) |
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Can you link the PRs in future and not commits? See other pipelines like here https://github.com/nf-core/sarek/blob/master/CHANGELOG.md
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| --fasta https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M32/GRCm39.primary_assembly.genome.fa.gz \ | ||
| --gtf https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M32/gencode.vM32.annotation.gtf.gz \ |
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If the pipeline only works with those files it makes sense to put these into the params?
| analysis pipeline. For information about how to interpret these results, please see the | ||
| <a href="https://nf-co.re/marsseq/1.0.3/output" target="_blank">documentation</a>. | ||
| <a href="https://nf-co.re/marsseq/1.0.3/docs/output" target="_blank">documentation</a>. |
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version needs to be bumped for a release
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| ## Metadata information | ||
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| The pipeline requires 3 additional files for experiment. |
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Can these xlsx files also be supplied as csvs?
| @@ -232,43 +232,46 @@ manifest { | |||
| homePage = 'https://github.com/nf-core/marsseq' | |||
| description = """MARS-seq v2 preprocessing pipeline""" | |||
| mainScript = 'main.nf' | |||
| nextflowVersion = '!>=23.04.0' | |||
| nextflowVersion = '!>=24.04.2' | |||
| version = '1.0.3' | |||
| version = '1.0.3' | ||
| doi = '10.1101/2023.06.28.546862, 10.5281/zenodo.8081210' |
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).