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varlociraptor workflow compatibility #23
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dlaehnemann
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… dna-seq-varlociraptor workflow
…ames, make wildcard names more descriptive
…d that times out the workflow
…ction definitions
…kflow to get entry point to work seamlessly
…stricted wildcards
…e situations in some settings
…e/snakemake#1841 for details of respective snakemake change)
…ile existence of the binary, not binary presence in path
…g_and_resources` is run, add logs to neo_fox rules
…nsolvable situations in some settings" This reverts commit 5e2c180.
… CPUs (and thus hampers workflow portability)
… upon writing into config file
… (hard-coded in the tool)
…andle empty entries, here
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This PR changes the column names in
config/samples.tsv
andconfig/units.tsv
to match those of thedna-seq-varlociraptor
Snakemake workflow. This way, parts of this workflow can be included as a module there, using the samesamples.tsv
andunits.tsv
prepared for that workflow.To make this work, the
samples.tsv
andunits.tsv
parsing incommon.smk
is adapted, as are wildcard names throughout the workflow. While at it, I also tried to make some wildcard names more descriptive and constrict more wildcards to the values they can actually take.