v1.4.0

1.4.0 (2024-12-04)

Features

• add slurm, cache, test scripts (4ab571f)
• bracken (8183326)
• cache rule (e7ac7bd)
• configfile (ebac6c0)
• do bracken on all taxonomic levels, only show species in multiqc (d8efee3)
• get the aggregated counts directly from subread (7f8900e)
• use col1 and col2 to see if it reduces ram usage (2f527c2)
• use subread from wrappers (e9971d8)

Bug Fixes

• add all the bracken files to the copy in /dev/shm (c4df691)
• dont use slurm within slurm , dumbass (acf4c57)
• get the correct featurecounts file (a2beada)
• handle manually subread sample renaming; corner case in csvtk (0a15ae8)
• put clean in the preprocess group (24be3b8)
• put fastq in the correct group (e6a3462)
• put slurm executor (f4b65f6)
• put tmp folders for index and map (a3c11ab)
• remove more mentions to coverm (900e667)
• remove tmp dirs if they exist (ccf4e09)
• rerun incomplete (99941d1)
• undo bracken copy (47f72eb)
• use proper featurecounts file (d76c680)

Performance Improvements

• cache but omit software versions (09eb311)
• disable groups (6d17ce8)
• double ram on subread join (f3c356f)
• put reads in a group and disable localrule (e7c2ad7)
• raise ram to tsv join (a06dcad)
• subread: raise ram to 4GB (b0ea99a)