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This PR changes the column names in config/samples.tsv and config/units.tsv to match those of the dna-seq-varlociraptor Snakemake workflow. This way, parts of this workflow can be included as a module there, using the same samples.tsv and units.tsv prepared for that workflow.

To make this work, the samples.tsv and units.tsv parsing in common.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.

dlaehnemann and others added 30 commits September 1, 2022 15:37
…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)
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3 participants