Jorge Langa

Add --remove-files on tarball creation

2

Add `--remove-files` on tarball creation ## Description Just added `--remove-files` flag to `tar` on the save section. This flag removes files on the fly as they are being added to...

Adding the `--remove-files` flag would prevent the following error: ``` Post job cleanup. /usr/bin/tar --posix -cf cache.tzst --exclude cache.tzst -P -C /home/runner/work/owner/repo --files-from manifest.txt --use-compress-program zstdmt zstd: error 70 :...

fix: Fix combine bracken outputs.py

1

This PR fixes the error #214 when different taxonomy ids have the same name, like: - Xylophagaidae: flies and molluscs - Plannococcus: bacteria and bug I did this by flipping...

feat: bowtie2 can now sort with samtools and picard

16

This PR shamelessly copies functionalities from bwa-mem2 to sort or not, do it by coordinate or queryname, and choose between samtools and picard to do so ### QC * [x]...