nf-core/funcscan
(Meta-)genome screening for functional and natural product gene sequences
ampamrantibiotic-resistanceantimicrobial-peptidesantimicrobial-resistance-genesargassemblybgcbiosynthetic-gene-clusterscontigsfunctionmetagenomicsnatural-productsscreeningsecondary-metabolites
Version history
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
toannotation_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
to1.2.0
(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
Photo by Jon Chan under CC BY-SA 2.0
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
Photo by Ra Boe under CC BY-SA 2.5