Kevin Chau

Secondary / accessory files as implicit inputs

1

Hello miniwdl team, I was wondering if there have been discussions around the implementation of inferring secondary/accessory files based on file inputs, similar to CWL's `secondaryFiles` option. E.g. in the...

Start and end coordinates switched - is this expected?

4

Output of `segmentrics` resulted in a call with `start` > `end` (`cnvkit==0.9.9`): Command: `cnvkit.py segmetrics -s -o --ci --bootstrap 100` Result: ``` chromosome start end gene log2 depth probes weight...

Bump zlib to v1.3

1

zlib 1.2.13's release zip has been pulled, use zlib13.zip

Smoothing window fraction fix results in noisier data in targeted sequencing panel?

1

We're currently evaluating an update from version 0.9.9 to 0.9.10. However, we're seeing some increased noise among the ratios and resulting in an increased rate of false positives. Specifically, looking...

Remove PyVCF dependency

1

Replace PyVCF, which has been abandoned for years now and can be buggy, with pysam, which offers stricter VCF parsing rules.