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nf-core/funcscan: Changelog

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

v1.1.5 - [2024-03-20]

Added

Fixed

  • #346 Pinned version of nf-validation to 1.1.3

Dependencies

Plugin Previous New version
Bakta 1.8.2 1.9.3
nf-validation Latest 1.1.3

Deprecated

v1.1.4 - [2023-11-07]

Added

Fixed

  • #306 Added new parameter annotation_prokka_retaincontigheaders to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
  • #307 Fixed stability of deepARG tests by using Zenodo copy of database (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133)
  • #310 Fixed error when supplying uncompressed input; added "fas" file extension for FASTA files. (by @tavareshugo)
  • #311 Merged pipeline template of nf-core/tools version 2.10. (by @jasmezz)

Dependencies

Tool Previous version New version
AMRFinderPlus 3.10.42 3.11.18
Bakta 1.7.0 1.8.2
MultiQC 1.14 1.15

Deprecated

  • FastQC

v1.1.3 - [2023-08-11]

Added

  • #290 Merged pipeline template of nf-core/tools version 2.9, updated references. (by @jfy133)
  • #285 Use nf-validation for samplesheet checking and added support for fna.gz input FASTA files. (by @louperelo, @mirpedrol, @jfy133)
  • #295 Add Prokka to MultiQC output. (by @louperelo)

Fixed

  • #296 Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz)
  • #297 Added check for empty annotation files prior going into screening. (❤️ to @alexhbnr for requesting, added by @jfy133)
  • #299 Fixed pigz error with symlinks in Pyrodigal. (by @jasmezz)
  • #300 Fixed wrong Pyrodigal channels being submitted to antiSMASH. (reported by Till Bayer, fix by @jasmezz)
  • #302 Removed trouble-causing default parameters in json schema. (by @robsyme)

Dependencies

Tool Previous version New version
comBGC 0.6.0 0.6.1
GECCO 0.9.2 0.9.8

Deprecated

v1.1.2 - [2023-06-30]

Added

Fixed

  • #279 Fix docker/podman registry definition for tower compatibility. (♥️ to sunitj for reporting, fix by @adamrtalbot)

Dependencies

Deprecated

v1.1.1 - [2023-05-24]

Added

  • #270 Merged pipeline template of nf-core/tools version 2.8 and updated modules accordingly. (by @jasmezz, @jfy133)
  • #274 Update all modules: changed docker links according to the change of quay.io as default repository and Pyrodigal annotation output now zipped. (by @jasmezz)
  • #275 Save DRAMP database in the common database directory if --save_databases is supplied. (by @jasmezz)

Fixed

  • #272 Fix typo in Prokka output path in modules.config. (by @jasmezz)
  • #273 Update Ampir module after input bugfix in module. (reported by @mathavanpu, fix by @louperelo)
  • #276 Fix Pyrodigal parameters in modules.config. (by @jasmezz)

Dependencies

Deprecated

v1.1.0 - British Beans on Toast - [2023-04-27]

Added

  • #238 Added dedicated DRAMP database downloading step for AMPcombi to prevent parallel downloads when no database provided by user. (by @jfy133)
  • #235 Added parameter annotation_bakta_db_downloadtype to be able to switch between downloading either full (33.1 GB) or light (1.3 GB excluding UPS, IPS, PSC, see parameter description) versions of the Bakta database. (by @jasmezz)
  • #249 Added bakta annotation to CI tests. (by @jasmezz)
  • #251 Added annotation tool: Pyrodigal. (by @jasmezz)
  • #252 Added a new parameter -arg_rgi_savejson that saves the file <samplename>.json in the RGI directory. The default ouput for RGI is now only <samplename>.txt. (by @darcy220606)
  • #253 Updated Prodigal to have compressed output files. (by @jasmezz)
  • #262 Added comBGC function to screen whole directory of antiSMASH output (one subfolder per sample). (by @jasmezz)
  • #263 Removed AMPlify from test_full.config. (by @jasmezz)
  • #266 Updated README.md with Pyrodigal. (by @jasmezz)

Fixed

  • #243 Compress the ampcombi_complete_summary.csv in the output directory. (by @louperelo)
  • #237 Reactivate DeepARG automatic database downloading and CI tests as server is now back up. (by @jfy133)
  • #235 Improved annotation speed by switching off pipeline-irrelevant Bakta annotation steps by default. (by @jasmezz)
  • #235 Renamed parameter annotation_bakta_db to annotation_bakta_db_localpath. (by @jasmezz)
  • #242 Fixed MACREL '.faa' issue that was generated when it was run on its own and upgraded MACREL from version 1.1.0 to 1.2.0 (by @Darcy220606)
  • #248 Applied best-practice error("message") to all (sub)workflow files. (by @jasmezz)
  • #254 Further resource optimisation based on feedback from 'real world' datasets. (ongoing, reported by @alexhbnr and @Darcy220606, fix by @jfy133)
  • #266 Fixed wrong process name in base.config. (reported by @Darcy220606, fix by @jasmezz)

Dependencies

Tool Previous version New version
Bakta 1.6.1 1.7.0

Deprecated

v1.0.1 - [2023-02-27]

Added

  • #229 Added pipeline DOI to WorkflowMain.groovy to display citation info when executing the pipeline. (by @jasmezz)

Fixed

  • #227 Removed a header check in the check_samplesheet.py script that was producing false negatives. Presence of required columns is still validated. (by @Midnighter)
  • #228 Improved database downloading guidance to emphasise it is recommended to let nf-core/funcscan do the downloading on a first run, rather than manually downloading yourself. (reported by @alexhbnr, fixed by @jfy133)

Dependencies

Deprecated

v1.0.0 - German Rollmops - [2023-02-15]

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

Added

  • Added annotation tools (Prokka, Prodigal, Bakta).
  • Added AMP screening workflow (tools: Macrel, AMPlify, ampir, hmmsearch).
  • Added ARG screening workflow (tools: ABRicate, AMRFinderPlus, DeepARG, fARGene).
  • Added BGC screening workflow (tools: antiSMASH, DeepBGC, GECCO, hmmsearch).
  • Added workflow summary tools (tools: hAMRonization, AMPcombi, comBGC).

Fixed

Dependencies

Deprecated