v1.3.39

What's Changed

• Updated to GL-get-workflow
  • Fix issue #12
    • Add pagination logic for GitHub releases to allow more than the default 30 results
  • Add support for nextflow workflows for Metagenomics and Amplicon

Full Changelog: v1.3.38...v1.3.39

v1.3.38

Update GL-est-rRNA-percentages

• Add additional organisms:
  • S. lycopersicum (tomato)
  • Salmonella
  • Saccharomyces
  • D. rerio (zebrafish)
  • Candida
  • Bacillus
  • Rhodopseudomonas palustris
• Updated rRNA reference dates to match latest retrieval date from NCBI (May 9, 2025)

v1.3.37

Update GL-est-rRNA-percentages with support for

• Klebsiella
• Burkholderia
• Updated dates to match latest downloaded versions used at GeneLab

v1.3.36

What's Changed

• Fix issue #5 - GL-file-association-table by @bnovak32 in #6

Full Changelog: v1.3.35...v1.3.36

v1.3.35

What's Changed

• Update handling of expected_suffix for single-end

Full Changelog: v1.3.34...v1.3.35

v1.3.34

• updates GL-get-genome-summary-wf to pull from a versioned release page, similar to GL-get-workflow
  • the genome summary workflow is still retained separately in its own download program because it is not an official GeneLab workflow like the others

v1.3.33

• updates internally used GeneLab programs to account for assay-specific suffixes that were added
  • GL-gen-file-associations-table, GL-validate-processed-data, and GL-gen-processed-data-readme`
• updates to GL-validate-raw-data to allow for more datatypes
• updates to GL-est-rRNA-perentages
  • added "--unlock" argument to be passed to snakemake call when needed
  • added ability to specify which reads to scan, and how many read-files per sample exist

v1.3.32

• updates to GL-get-workflow
  • added a --list-available-versions flag (previously this list could only be seen if requesting a version that didn't exist)
  • workflow name letters that are tied to the protocol (e.g., the "-F" in "NF_RCP-F") are no longer hard-coded, so all versions with tagged releases can be pulled at any time

v1.3.31

• updating GL-est-rRNA-percentages
  • added --directRNAseq flag for when input reads are RNA sequences with Us instead of Ts
    • this makes temp read files with U's converted to T's prior to passing to hts_SeqScreener, as that won't allow U's (temp files are made instead of streaming from a pipe because I couldn't figure out how to get hts_SeqScreener to take the start from standard in even for 1 input, letalone if there were paired-ends)

v1.3.30

includes updates integrated by @asaravia-butler

• updates to GL-est-rRNA-percentages

  • added L. boulardi
  • added options for designating specific nodes for processing, excluding nodes, and specifying queue when using slurm

• updates to GL-validate-raw-data

  • added options for designating specific nodes for processing, excluding nodes, specifying queue, and allocating memory when using slurm
  • added --HRremoved-suffix as an acceptable GeneLab suffix for raw fastq files
  • added additional acceptable R1 and R2 suffixes for original fastq files
  • added additional acceptable R3 suffixes for ATACseq datasets
  • increased memory usage for JAVA