fix: fix somatic snappy (#477) #491
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…on using filter_list
…ipeline into 477-fix-somatic-snappy
…BFilter and those which aren't, and removed parallelization of EBFilter
…step documentation
mbenary
approved these changes
Mar 18, 2024
docs/somatic_cnv.rst
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| Somatic variant calling is implemented differently for exome and whole genome data. | ||
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| The whole genome data "branch" is currently under review, as GRCh38 support in ``Control-FREEC`` (the main workhorse for WGS CNV calling) is not complete. | ||
| CNV calling in WGS data can aslo be done using ``cnvkit``, but its pipeline implementation is also incomplete. |
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typo in "can also be done"
| for i, t in ((1, 1), (2, 1), (2, 2)) | ||
| for ext in ("log", "conda_list.txt", "conda_info.txt") | ||
| for chksum in ("", ".md5") | ||
| for mapper in ("bwa",) |
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Is "mapper" actually used? There is no {mapper} in tpl .
| .. note:: | ||
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| The step requires a ``cancer_matched`` configuration & samplesheet files. | ||
| This is an unnecessary requirement, as might be dropped in the future. |
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Typo: "as might" ... better "which might"
| pattern: "V5_noUTR" | ||
| path: <absolute path to the Agilent V5 bed file> | ||
| - name: Agilent SureSelect V5 + UTRs" | ||
| patten: "V5_UTR" |
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Typo: "patten" vs "pattern"
This was referenced Dec 9, 2024
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The dreaded mega-PR is there!
It fixes most of the known snappy issues for the somatic branch.
There are a few glitches left with log files (that are in
work, but not inoutputfor example), but a generic fix would be warranted (rather than a lot of fixes in each wrapper).Documentation is also improved (or at least completed): a somatic overview is there, and some steps are more clearly described. But again, there is still much to do.