v1.5.0

1.5.0 (2025-05-13)

Features

• add bracken by level (c6a0fb1)
• bracken: separate bracken and kraken. report only bracken files (7176fb8)
• gzip on the fly (343a63c)
• kraken2 at the speed of light (1113bf8)
• kraken2 at the speed of light (8cc0d31)
• kraken2: merge libraries prior to assinging taxonomies (86e73d3)
• prokaryotes/cluster: use bgzip instead of pigz when fasta files are involved (b851c58)
• Put bowtie2 files separated by host in different folders (6e54529)

Bug Fixes

• add env with seqtk (d120b73)
• add fasta header cleanup step (3ebe042)
• add htslib (39404ca)
• add missing separator (48702a7)
• ask for emptyness in condense (7a0aa54)
• better filenames (2b5b018)
• cat has no verbose (41fece6)
• compress instead of mv (0e0c26e)
• compute only some levels for beta-diversity, remove messages that should go to stderr in alpha_diversity (704f8b1)
• correct log (b388503)
• correct paths (3709b86)
• csvtk (e85b353)
• decompress fasta (ec41c89)
• delete output folder if it exists (3b36705)
• disable groups (558f8fe)
• disable groups because they seem to break the pipeline (bcb328a)
• disable localrule because it interferes with groups (b760aa0)
• double ram on checkm2 (9a5b963)
• drop duplicates in sample_library (848a5c3)
• escape sed expression and remove cat (a2e6c90)
• fix renaming of bins after magscot (85e3755)
• generate one quast report per assembly so multqc does not aggregate them (2b2d7c4)
• get bracken reports, use them in multiqc, split kraken2 and bracken envs (c39c592)
• get only one bracken report and use it for multiqc. delete the rest (d7561ac)
• go back to dram 1.4.6 (c7439ab)
• handle better logs (07a29e6)
• keep order in parallel to avoid race condition when printing (cfebd83)
• mention to wrong variable (5e07df5)
• mention to wrong variable, again (d1efb29)
• missing commas (3d83c13)
• missing extension (193e6a7)
• outputs in correct place (056f5aa)
• pin dram to 1.4.6 (9ad0212)
• pin mamba to 1 to fix virsorter2 conda installation that does on execution (804c2da)
• please pre-commit (9f079ff)
• prefix (94e9514)
• process substitution because dram can't handle fa.gz (e9bb93b)
• prokaryotes: generate one quast report per assembly so multqc does not aggregate them (89df113)
• put all the aggregations together in a for loop (2109bf6)
• remove double curly brackets (abf3310)
• remove double curly brackets, again (43c1a40)
• remove import (8f1db2e)
• remove shadow because it slows down everything (f5e478c)
• remove split (740a0aa)
• run coverm contig over viruses instead of genome, since there is no binning done (7d41a65)
• separate host in path (d62ae0d)
• tell csvtk explicitelly to use tabs (01d77e5)
• try to delete out folder (a8fc1c7)
• typo (a178f4d)
• use bracken level files in report (8967589)
• use full filenames in multiqc (82bfd0e)
• use the new variable (11455b6)

Performance Improvements

• accelerate bgzipping (54fe677)
• accelerate bgzipping, again (1b9a027)
• checkm2: double ram on failure, retry 5 times (bb5f51e)
• double ram on dram distill (fc909a0)
• multiqc: update wrapper (742f99c)
• raise ram just in case (596cb95)
• raise ram just in case (68e545a)
• raise ram just in case (1faefc3)
• raise threads (82f1d84)
• raise time for virsorter2 (8827d46)
• remove job grouping on every file (f6a127f)
• remove job grouping on megahit (6597dbb)
• use shadow on singlem pipe to see if it fixes it (a4e17e1)
• use temp directory as output (207d537)