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CHANGELOG.md

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nf-core/predictorthologs: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.0dev - [date]

Initial release of nf-core/predictorthologs, created with the nf-core template.

Added

  • Updated infrastructure files to nf-core/tools version 1.9
  • Added option for --input_is_protein
  • Added option for --differential_hash_expression performed by scikit-learn's Logistic Regression
  • Added option of using sourmash to search instead of DIAMOND. This stays in hash-land by searching hashes (provided by --hashes or found by --differential_hash_expression) directly into a sourmash sequence bloom tree index database
  • Added option for bam deduplication, if you wish to skip deduplication step add the -skip_remove_duplicates_bam flag
  • Added ability to search DIAMOND for hashes that were unassigned from sourmash (#79)
  • Add version printing for sencha, and sourmash, update versions in environment.yml (#88)

Fixed

  • Differential hash expression
    • Output differential hash expression hashes and DIAMOND blastp search results into a per-group subfolder
    • Add --with-abundance flag to allow for differential expression with tracked abundances
  • hash2kmer.py ignores empty lines
  • Fixed polyX trimming for paired-end fastqs (#66)
  • Fixed paired-end reads getting removed after trimming (#75)
  • Fixed number of cpus, memory, time requirements for sambamba processes (#76)
  • Fixed noncoding search to use cmscan instead of cmsearch from INFERNAL (#74)
  • Propagate molecule and k-mer size to sample id after translate
  • Add version printing for sencha, and sourmash in Dockerfile, update version of sencha

Dependencies

  • Added 7z (bioconda==p7zip=15.09) to deal with compatibilities of bioconda's unzip the taxdmp.zip file from NCBI: (#14)
  • Added rsync to download NCBI RefSeq releases
  • Actually installed rsync via apt in Dockerfile, not just unzip (#16)
  • Added bedtools=2.29.2 to dependencies
  • Added Rust (required for compiling sourmash from GitHub) (#24)
  • Added pandas=1.0.3, scikit-learn=0.22.1, and sourmash=3.2.2 to dependencies
  • Added subread=1.6.4 (featurecounts) and bioawk=1.0
  • Updated MultiQC to version 1.8 to avoid annoying YAML errors
  • Add ripgrep=12.0.1 (faster than all other greps) to dependencies
  • Updated sourmash=3.3.0 (#46) to support zip files as indices
  • Added csvtk=0.20.0 to dependencies
  • Addeed infernal=1.1.2 to dependencies
  • Update DIAMOND to version 0.9.35 to deal with new NCBI taxonomy formats
  • Added sambamba=0.7.1 using bioconda channel
  • Updated sencha=1.0.3 to fix the bug in memory errors possibly with the numpy array on unique filenames (PR #96 on sencha)

Deprecated