Published March 5, 2025 | Version 2.1.0
Software Open

nf-core/funcscan: v2.1.0 - Egyptian Koshari - 2025-03-05

Creators

  • 1. Leibniz Institute for Natural Product Research and Infection Biology – HKI
  • 2. HKI Jena, MPI-EVA Leipzig
  • 3. Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie - HKI
  • 4. Big Data Biology Lab
  • 5. University of Cambridge
  • 6. @ScilifelabDataCentre
  • 7. @seqeralabs
  • 8. Seqera
  • 9. Seqera Labs

Description

v2.1.0 - Egyptian Koshari - [2025-03-05]

Added

  • #421, #429, #433, #438, #441 Updated to nf-core template 3.0.2, 3.1.0, 3.1.1, 3.1.2, and 3.2.0. (by @jfy133 and @jasmezz)
  • #427 AMPcombi now can use multiple other databases for classifications. (by @darcy220606)
  • #428 Added InterProScan annotation workflow to the pipeline. The results are coupled to AMPcombi final table. (by @darcy220606)
  • #431 Updated AMPcombi, Macrel, all MMseqs2 modules, MultiQC, Pyrodigal, and seqkit, added --taxa_classification_mmseqs_compressed parameter. (by @jasmezz)
  • #441 Updated MultiQC. (by @jasmezz and @jfy133)
  • #440 Updated Bakta and introduced new parameter --annotation_bakta_hmms. (by @jasmezz)

Fixed

  • #427 Fixed the AMP reference database issues reported by users, due to non-ASCII characters. (by @darcy220606)
  • #430 Updated rgi/main module to fix incorrect variable name. (by @amizeranschi and @jasmezz)
  • #435 Fixed dependency errors within taxonomy merging scripts, updated the code and output for all three workflows. Bumped to version 0.1.1. (by @darcy220606)
  • #437 Fixed file name error when supplying already preprocessed CARD database for ARG workflow. (by @jasmezz)
  • #446 Updated antiSMASH modules to fix apptainer execution. (by @jasmezz and @jfy133)
  • #448 Fixed taxonomy merge to work with output from GTDB/SILVA/KALAMARI. (by @darcy220606)
  • #447 Added --annotation_pyrodigal_usespecialstopcharacter parameter to improve AMPlify screening. (by @jasmezz)
  • #454 Updated default CPU requirement of ampcombi2/parsetables. (by @jasmezz)

Dependencies

| Tool | Previous Version | New Version | | ------------ | ---------------- | ----------- | | AMPcombi | 0.2.2 | 2.0.1 | | Bakta | 1.9.3 | 1.10.4 | | InterProScan | - | 5.59_91.0 | | Macrel | 1.2.0 | 1.4.0 | | MMseqs2 | 15.6f452 | 17.b804f | | MultiQC | 1.24.0 | 1.27 | | Pyrodigal | 3.3.0 | 3.6.3 | | seqkit | 2.8.1 | 2.9.0 |

Deprecated

Photo by <a href="//commons.wikimedia.org/wiki/User:Dinapriv" title="User:Dinapriv">Dina Said </a> - <span class="int-own-work" lang="en">Own work</span>, <a href="https://creativecommons.org/licenses/by-sa/4.0" title="Creative Commons Attribution-Share Alike 4.0">CC BY-SA 4.0</a>, <a href="https://commons.wikimedia.org/w/index.php?curid=36970215">Link</a>

Files

nf-core/funcscan-2.1.0.zip

Files (2.1 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/funcscan/tree/2.1.0 (URL)

Software

Repository URL
https://github.com/nf-core/funcscan