Review comments #589
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Review comments #589
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rannick
approved these changes
Mar 3, 2025
| @@ -90,7 +90,7 @@ For more details and further functionality, please refer to the [usage documenta | |||
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| ## Credits | |||
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| genomic-medicine-sweden/nallo was originally written by Felix Lenner. | |||
| genomic-medicine-sweden/nallo was originally written by [Felix Lenner](https://github.com/fellen31). | |||
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| We thank the following people for their extensive assistance in the development of this pipeline: [Anders Jemt](https://github.com/jemten), [Annick Renevey](https://github.com/rannick), [Daniel Schmitz](https://github.com/Schmytzi), [Lucía Peña-Pérez](https://github.com/Lucpen), [Peter Pruisscher](https://github.com/peterpru) & [Ramprasad Neethiraj](https://github.com/ramprasadn). | |||
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Do you want to change the order here too?
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No, I'll go with the first-name sort, and have a minimum two commits/review policy to be added in the readme 😄
fellen31
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Mar 3, 2025
* bump version (#530) * Add credits (#531) * Add missing credits * update changelog * Assemble ONT genomes (#516) * Assemble ONT genomes * hifiasm 0.24.0 * update tests * update patch * Template update for nf-core/tools version 3.1.1 (#532) * Initial template commit * Template update for nf-core/tools version 3.1.2.dev0 * Template update for nf-core/tools version 3.1.1 * changelog * merge mistake * merge mistake * merge mistake * merge mistakes * fix lint * update ci * fix version * fix tests * fix RO crate * remove nf-core reference * bump deepvariant version (#535) * Output per-base depth in d4 format (#537) * output per-base depth in d4 format * Changelog * update nf-core module * Downgrade to Sniffles1 (#536) * Downgrade to Sniffles1 * Update CHANGELOG.md * bump deepvariant version (#535) * fix readme * Add skip for SV calling * Template sync 3.1.2 (#541) * Initial template commit * Template update for nf-core/tools version 3.1.2.dev0 * Template update for nf-core/tools version 3.1.2.dev0 * Template update for nf-core/tools version 3.1.2.dev0 * Template update for nf-core/tools version 3.1.1 * Template update for nf-core/tools version 3.1.1 * use ro-crate command * changelog * update workflow dependencies * make sv filtering conditional on skip_sv_calling param * style: fix text alignment * style: fix linting issue * update changelog * fix linting issues in CHANGELOG.md param table * Run CI tests with latest-stable version of Nextflow (#545) * Run CI tests with latest-stable version of nextflow * Changelog * Fix naming mistakes in output docs (#546) * Fix naming mistakes in output docs * Changelog and prettier * Update docs/output.md Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> * prettier --------- Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> * change vcf headers, merge by sample, merge by case, first draft for merging paraphase json * add script to merge json files * update changelog * fixes * add arg for bcftools query * add prefix to CREATE_SAMPLES_FILE * use arg2 * modify create_sample_files to add the haplotype in the sample name * haplotype specific sample names, force single * Fix naming for SNVs and pipeline not running with (#556) * create empty channels to use * update paraphase * updated snapshots * update snapshots * Update CHANGELOG.md Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/local/merge_json.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/local/merge_json.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update conf/modules/call_paralogs.config Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update conf/modules/call_paralogs.config Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/local/merge_json.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * case to family and aligned bracket * multi-argument formatting * use groupTuple * add merge json * add executing permissions to script * update script * update script * update script * add to software references * fix config issue * remove snapshots * update snaphshots * exclude vcf and tbi unpublished * update snaps * remove snap * add publish dir * update snap * revert change * paralogs false default publish, remove publishing for all but family merged vcf * use family_id directory * prettier * updated modules added * update output.md * publish family json * update snapshots * use sample and family directories, update mapping for family merging * update snapshots * Update docs/output.md Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * prettier * Limit VEP to 1 cpu while bugged (#558) * Bump Severus to 1.3 (#557) * Bump Severus version * Update CHANGELOG.md * Always run all SV callers (#542) * Downgrade to Sniffles1 * Update CHANGELOG.md * bump deepvariant version (#535) * Always run multiple SV-callers * changelog * changelog * update tests and ci * Also output CNV-calls * CHANGELOG * update conf * wip * update docs+tests * remove rouge versions.yml * Template update to v3.2.0 (#560) * Initial template commit * Template update for nf-core/tools version 3.1.2.dev0 * Template update for nf-core/tools version 3.1.1 * Template update for nf-core/tools version None * Template update for nf-core/tools version None * CHANGELOG * Patch to dev (#565) * Fix pipeline can't run without * CHANGELOG * docs * docs * update snaps * fix CI * Update CHANGELOG.md * changelog date * Add vep_plugin_files to files check * CHANGELOG * Update CHANGELOG.md * always failing CI because of nf-core update * Replace dipcall (#566) * wip * Replace dipcall * Replace dipcall * description * Update CHANGELOG * ignore bam md5 * CHANGELOG * Update main.nf * Update workflows/nallo.nf Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> --------- Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> * Fix filter SNVs tries to run even with --skip_snv_calling (#570) * Fix filter SNVs tries to run even with --skip_snv_calling * CHANGELOG * Update CHANGELOG.md * Fix unsorted sniffles1 variants (#572) * Fix unsorted sniffles1 variants * update tests * Update metro map (#573) * CHANGELOG * Add contributors to `nextflow.config` (#574) * Add contributors to config * Add missing * Fix a few language server issues (#533) * start fixing language server issues * revert some changes, remove encode * fix some more * Update main.nf * update methylation tests * Fix nextflow.config issues (#578) * Fix sniffles1 (#580) * Fix sniffles1 * fix lint * Add missing nf-test triggers * update snaps * remove missed dipcall references (#577) * Merge master into dev (#576) * Fix pipeline not running without `--vep_cache` (#553) * Fix pipeline can't run without * CHANGELOG * docs * docs * update snaps * fix CI * Update CHANGELOG.md * changelog date * Add vep_plugin_files to files check * CHANGELOG * Update CHANGELOG.md * always failing CI because of nf-core update * CHANGELOG * Update CHANGELOG.md * Fix project samplesheet validation (#584) * Fix mistake in usage docs (#586) * Update usage.md * changelog * Prep release 0.5.0 (#585) * Bump version 0.5.0 * CHANGELOG * update snaps * Review comments (#589) --------- Co-authored-by: padraicc <padraic.corcoran@scilifelab.uu.se> Co-authored-by: Pádraic Corcoran <padraicc@users.noreply.github.com> Co-authored-by: padraicc <padraic.corcoran£scilifelab.uu.se> Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> Co-authored-by: Annick Renevey <annick.renevey@scilifelab.se>
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,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).