new subworkflow - fastq shortreads preprocess qc#9665

Merged

vagkaratzas merged 40 commits intomasterfrom

fastq_shortreads_preprocess_qc

Feb 3, 2026

Commits on Jan 14, 2026

clumpify added, cat_fastq added, nf-test added for missing tools
vagkaratzas
committed
Update WHATSHAP/PHASE container, topic versions and task.cpus (#9642)

eliottBo
authored and
vagkaratzas
committed
Feature/localcdsearch (#9632)

committed
Update RGI modules to be Nextflow strict syntax compliant (#9650)

authored and
vagkaratzas
committed
Generate normalised matrix with `variancepartition/dream` (#9645)

delfiterradas
authored and
vagkaratzas
committed
Add draft of FASTQ_REMOVE_ADAPTERS_AND_MERGE subworkflow with tests (#9521)

committed

Commits on Jan 20, 2026

Commits on Jan 22, 2026

Commits on Feb 2, 2026