docs: Check & update of configuration defaults (first part) #532
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I think having all these examples will be really helpful to people getting started with the pipeline (in the CUBI environment)!
The config yamls generated will have quite long lines, though ;) but I'd rather have very long comments providing information and context than no information at all.
| features: | ||
| path: /data/cephfs-1/work/projects/cubit/current/static_data/annotation/GENCODE/19/GRCh37/gencode.v19.annotation.gtf | ||
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| # Step Configuration ============================================================================== |
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While we're at it, we can correct the headers, which all just say "Step Configuration"
| # static_data_config: | ||
| # cosmic: | ||
| # path: /data/cephfs-1/work/projects/cubit/current/static_data/db/COSMIC/v90/GRCh38/CosmicAll.vcf.gz | ||
| # dbnsfp: | ||
| # path: /data/cephfs-1/work/projects/cubit/current/static_data/db/dbNSFP/3.5/GRCh38/dbNSFP.txt.gz | ||
| # dbsnp: | ||
| # path: /data/cephfs-1/work/projects/cubit/current/static_data/db/dbSNP/b147/GRCh38/common_all_20160407.vcf.gz | ||
| # reference: | ||
| # path: /fast/work/groups/cubi/projects/biotools/static_data/reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa | ||
| # features: | ||
| # path: /fast/work/groups/cubi/projects/biotools/static_data_by_ref/GRCh38/annotation/GENCODE/36/gencode.v36.primary_assembly.annotation.gtf |
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These are just the GRCh38 version for static_data_config defaults, correct? That should be mentioned in the description.
| @@ -43,6 +43,9 @@ class TargetCoverageReportEntry(SnappyModel): | |||
| - name: IDT_xGen_V1_0 | |||
| pattern: "xGen Exome Research Panel V1\\.0*" | |||
| path: "path/to/targets.bed" | |||
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| Bed file for many Agilent exome panels can be found in | |||
| /fast/work/groups/cubi/projects/biotools/static_data/exome_panel/Agilent | |||
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The existing comment (not the one you added) seem to be incorrect, as I'm quite sure the path will be mapped to the name "IDT_xGen_V1_0" not "default" ;)
And I'm also not sure whether the pattern actually matches what the description claims.
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I'm not sure what you mean here: the pattern is a correct (albeit strange) regular expression, and a biomedsheet entry matching such pattern is associated with the name, which is finally mapped to a path.
| path_baits: str | ||
| """ | ||
| Different exome panels cannot be accomodated here, because the selection method used for coverage is not used. |
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It means that the target_coverage sub-step will pick the name of the panel from the Samplesheet, and then map it to some actual files using this weird mapping scheme implemented in the __init__.py code. This allows multiple exome kits within the same dataset.
It is not the case with the path_baits in the somatic/mbcs bit. Here, we directly point to the exome kit bed file. There is no querying the samplesheet.
First attempt. Only ngs_mapping & somatic_variant calling are used.
IMPORTANT NOTE: The default config is now out of sync with the STAR environment version. Is that OK to change the STAR version in the wrapper's environment, or should I create another PR?