Release 0.5.0 #581
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Release 0.5.0 #581
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* Add missing credits * update changelog
* Assemble ONT genomes * hifiasm 0.24.0 * update tests * update patch
* 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
* output per-base depth in d4 format * Changelog * update nf-core module
* Downgrade to Sniffles1 * Update CHANGELOG.md * bump deepvariant version (#535) * fix readme
* 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
* Run CI tests with latest-stable version of nextflow * Changelog
Add skip for SV calling
* 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>
…erging paraphase json
* Bump Severus version * Update CHANGELOG.md
* 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
* 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
* 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
* 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 * CHANGELOG * Update CHANGELOG.md
* Fix unsorted sniffles1 variants * update tests
* Add contributors to config * Add missing
* start fixing language server issues * revert some changes, remove encode * fix some more * Update main.nf * update methylation tests
* Fix sniffles1 * fix lint * Add missing nf-test triggers * update snaps
* 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
Merge master into dev
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* Update usage.md * changelog
* Bump version 0.5.0 * CHANGELOG * update snaps
peterpru
approved these changes
Mar 3, 2025
peterpru
reviewed
Mar 3, 2025
docs/index.md
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| @@ -93,7 +92,7 @@ For more details and further functionality, please refer to the [usage documenta | |||
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| genomic-medicine-sweden/nallo was originally written by Felix Lenner. | |||
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Suggested change
| genomic-medicine-sweden/nallo was originally written by Felix Lenner. | |
| genomic-medicine-sweden/nallo was originally written by [Felix Lenner](https://github.com/fellen31). |
rannick
approved these changes
Mar 3, 2025
| @@ -93,7 +92,7 @@ For more details and further functionality, please refer to the [usage documenta | |||
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| genomic-medicine-sweden/nallo was originally written by Felix Lenner. | |||
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| We thank the following people for their extensive assistance in the development of this pipeline: | |||
| 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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Is this the order of the most contribution? I see it is alphabetical, but maybe Daniel should be higher?
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I hate to be the judge of who has contributed most 🙈 Even if it means you are listed second!
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So yes, it's alphabetical.
| | `svs/family/{family_id}/{family_id}_svs_merged.vcf.gz.tbi` | Index of the merged VCF file | :white_check_mark: | | | | ||
| | `svs/family/{family_id}/{family_id}_cnvs_svs_merged.vcf.gz` | VCF file with merged CNVs and SVs per family | | | :white_check_mark: | | ||
| | `svs/family/{family_id}/{family_id}_cnvs_svs_merged.vcf.gz.tbi` | Index of the merged VCF file | | | :white_check_mark: | | ||
| SV and CNV calls are output unmerged per sample, while the family files are first merged between samples for SVs and CNVs separately, then the merged SV and CNV files are merged again, with priority given to coordinates from the SV calls. SV calls are output for all callers, but only variants from one caller (set by `--sv_caller`) are merged with CNVs, then annotated, ranked and filtered. |
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Would a little asterisk in the metro map help user understand the behaviour (but this doc is so clean that consider this very optional)
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I have thought of the metro-map as a basic overview of the pipeline (not all steps are included there). This is complicated, but I think I would rather keep the metro-map on the cleaner side.
I think we will need to give this an overhaul at some point, e.g. being able to use several callers simultaneously, but also be able to filter out calls on a per-caller level.. So at that point I can draw up a schematic for this, to make it more clear.
| @@ -18,12 +17,13 @@ process SPLIT_BED_CHUNKS { | |||
| // Chunk size needs to be > 0. Where to specify a needed argument? params? | |||
| // Will not output more regions than in file, even if chunk_size > number of regions | |||
| script: | |||
| def VERSION = "1.0" | |||
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Add comment specifying when that needs to be updated?
| contribution: ['author','maintainer'], | ||
| orcid: 'https://orcid.org/0000-0002-9594-0710' | ||
| ], | ||
| ] |
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Here I would order in descending order of contribution, not ascending
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Completely unordered here!
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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).