Release 0.1.0 #90
Release 0.1.0 #90
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…ngle element channels
Full size test fails because only `BCFTOOLS_NORM_SINGLESAMPLE` and not `BCFTOOLS_NORM` was actually decomposing variants.
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| parameters: | ||
| - "" |
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A test with no parameters?
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Yes, so to run the -profile test with no extra arguments.
CHANGELOG.md
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| 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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| ## v1.0dev - [date] | ||
| ## v0.1.0 - [date] |
| } | ||
| withLabel:process_high_memory { | ||
| memory = { check_max( 200.GB * task.attempt, 'memory' ) } | ||
| memory = { check_max( 218.GB * task.attempt, 'memory' ) } | ||
| } | ||
| withLabel:error_ignore { | ||
| errorStrategy = 'ignore' |
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Does nallo processes need that much more than the standard compute? I would usually not meddle with the base config but specify per module in modules.config if some modules need extra.
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Some need a lot to merge many samples, but I should keep this label 200.
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Massive work @fellen31 ⭐
As you write in the PR description their are some workflows that would benefit from a refactoring. Also, quite a few of the local modules uses your private dockerhub, let's see if we can shift a few of those in the next release.
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Would be good to rework some of the more deeply nested if statements.
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Yes! General preference between using if/switch statements in workflow vs ext.when?
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Here I we could branch out into more subworkflows. But otherwise, it's a balance... I kind of prefer the ext.when from an aesthetic point of view, but then I had people complaining that it wasn't clear from the code what was happening 😅
subworkflows/local/snv_annotation.nf
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| // Index and normalize single sample vcfs | ||
| BCFTOOLS_INDEX_SINGLESAMPLE(ch_single_sample_vcf) | ||
| ss = ch_single_sample_vcf.join(BCFTOOLS_INDEX_SINGLESAMPLE.out.csi) |
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guessing that ss is "single sample" but it would be good to have a more explicit channel name.
| // Collect GVCFs | ||
| ch_snp_calls_gvcf = ch_snp_calls_gvcf.mix(DEEPVARIANT.out.gvcf) | ||
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| // TODO: This only works with DeepVariant for now (remove PEPPER_MARGIN_DEEPVARIANT/Deeptrio?) |
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
* Add review suggestions + full test changes
* Update CODEOWNERS Change the code-owners to the GitHub team. This way we can more easily change the team and not having to update the CODEOWNERS * Fixed org
* Update whatshap stats version to avoid ZeroDivisionError * Update release date
This PR aims to make a pre-release of the pipeline, which is on the whole, functional.
There's still lots of things I would like to fix before a 1.0 release though. Including going through each subworkflow and updating/tidying it. At the same time, it would be good to have a version of the pipeline since some data will be generated with it before 1.0.
So there are a number of things this PR does not concern itself with, that I aim to adress in future releases:
General:
Subworkflows:
Modules:
PR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).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).