[TheiaCoV/TheiaProk/TheiaMeta/TheiaEuk/Freyja_FASTQ] `fastq-scan` updates & improvements. Adding JSON as wf output file#662

Merged

AndrewLangvt merged 19 commits intomainfrom cjk-fastq-scan-json-outputs

Nov 8, 2024

+134-59

Commits on Oct 22, 2024

lots of updates to fastq_scan_pe task: upgrade to fastq-scan 1.0.1; reduce disk to 50gb and cpu to 1; added set -euo pipefail; removed capture of date; added debug statements to cleanup STDOUT/logs…
kapsakcj
committed
similar changes also made to fastq_scan_se task: updated docker image; reduced disk to 50gb and cpu to 1; added set -euo pipefail; added DEBUG statements and cleaned up STDOUT for clear log files; …
kapsakcj
committed

Commits on Oct 28, 2024

Merge remote-tracking branch 'origin/main' into cjk-fastq-scan-json-outputs
kapsakcj
committed

Commits on Oct 30, 2024

Commits on Nov 7, 2024

update CI for snippy_variants task
kapsakcj
committed