Minor Release - Version 1.5.0#300
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Prepare for 1.5.0dev
Update rtgtools
move bcftools and tabix to nf-core
…-heder Replace SORT_BED and REFORMAT_HEADER with nf-core modules
fixing bugs in bndeval outputs and ensemble analysis
add rtg cnveval as benchmark method for copynumber variants
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
jfy133
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jfy133
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To speed up the review, I've not checked:
- Python scripts (as I don't know really know the language)
- For all modules I only checked
environment.ymlfor version bumps not listed in CHANGELOG - I've not checked the
meta.yamlof modules/subworkflows as we aren't really using them for anything yet in nf-core ;)
No blockers AFAICS, but just to double check given you had quite a few module deletion etc, there is no changes to output files etc. that requires an update to output./md?
| "id": "test_intersect", | ||
| "caller": "manta" | ||
| }, | ||
| "test_intersect.truth.manta_TP_base.bed:md5,d41d8cd98f00b204e9800998ecf8427e" |
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That was not a good intersection example, no TP produced. I will try to have a better example.
| "id": "test_intersect", | ||
| "caller": "manta" | ||
| }, | ||
| "test_intersect.truth.manta_TP_comp.bed:md5,d41d8cd98f00b204e9800998ecf8427e" |
| @@ -4,6 +4,4 @@ channels: | |||
| - conda-forge | |||
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| // apply sompy for small somatic variant benchmarking | ||
| HAPPY_SOMPY( | ||
| input_ch.map{meta, test, test_index, truth, truth_index, regions, target -> [meta, test, truth, regions, target]}, | ||
| input_ch.map{meta, test, test_index_, truth, truth_index_, regions, target -> [meta, test, truth, regions, target]}, |
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| input_ch.map{meta, test, test_index_, truth, truth_index_, regions, target -> [meta, test, truth, regions, target]}, | |
| input_ch.map{meta, test, _test_index, truth, _truth_index, regions, target -> [meta, test, truth, regions, target]}, |
Shouldn't it be this way around? :think
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it looks weird indeed 🗡️
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I cannot commit your suggestions directly unfortunately (since dev is protected).
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| compressed_ch = ch_inputs.compressed.join(TABIX_TABIX_2.out.index) | ||
| vcf_ch = TABIX_BGZIPTABIX.out.gz_index.mix(compressed_ch) |
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I have a feeling now you have a particular system for these, so you can probably disregard all my previous comments if you have a particular pattern for putting _ch at the end
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I can confirm you can merge/release once #301 merged into |
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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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).