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

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 Dina Said - Own work, CC BY-SA 4.0

v2.0.0 - Brazilian Escondidinho - 2024-09-05

v2.0.0 - Brazilian Escondidinho - [2024-09-05]

Breaking change

• #391 Made all "database" parameter names consistent, skip hmmsearch by default. (by @jasmezz)

Old parameter	New parameter
annotation_bakta_db_localpath	annotation_bakta_db
arg_abricate_db	arg_abricate_db_id
arg_abricate_localdbdir	arg_abricate_db
arg_deeparg_data	arg_deeparg_db
arg_deeparg_data_version	arg_deeparg_db_version
arg_rgi_database	arg_rgi_db
bgc_antismash_databases	bgc_antismash_db
bgc_antismash_installationdirectory	bgc_antismash_installdir
bgc_deepbgc_database	bgc_deepbgc_db
save_databases	save_db
taxa_classification_mmseqs_databases_localpath	taxa_classification_mmseqs_db
taxa_classification_mmseqs_databases_id	taxa_classification_mmseqs_db_id
taxa_classification_mmseqs_databases_savetmp	taxa_classification_mmseqs_db_savetmp
amp_skip_hmmsearch	amp_run_hmmsearch
bgc_skip_hmmsearch	bgc_run_hmmsearch

• #343 Standardized the resulting workflow summary tables to always start with 'sample_id\tcontig_id\t..'. Reformatted the output of hamronization/summarize module. (by @Darcy220606)
• #411 Optimised hAMRonization input: only high-quality hits from fARGene output are reported. (by @jasmezz, @jfy133)

Added

• #322 Updated all modules: introduce environment.yml files. (by @jasmezz)
• #324 Removed separate DeepARG test profile because database download is now stable. (by @jasmezz)
• #332 & #327 Merged pipeline template of nf-core/tools version 2.12.1 (by @jfy133, @jasmezz)
• #338 Set --meta parameter to default for Bakta, with singlemode optional. (by @jasmezz)
• #343 Added contig taxonomic classification using MMseqs2. (by @Darcy220606)
• #358 Improved RGI databases handling, users can supply their own CARD now. (by @jasmezz)
• #375 Merged pipeline template of nf-core/tools version 2.14.1. (by @jfy133)
• #381 Added support for supplying pre-annotated sequences to the pipeline. (by @jfy133, @jasmezz)
• #382 Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. (by @jfy133, @Darcy220606)
• #366 Added nf-test on pipeline level. (by @jfy133, @Darcy220606, @jasmezz)
• #403 Added antiSMASH parameters --pfam2go, --rre, and --tfbs. (reported by @Darcy220606, added by @jasmezz)
• #405 Added argNorm to ARG subworkflow. (by @Vedanth-Ramji)

Fixed

• #348 Updated samplesheet for pipeline tests to 'samplesheet_reduced.csv' with smaller datasets to reduce resource consumption. Updated prodigal module to fix pigz issue. Removed tests/ from .gitignore. (by @Darcy220606)
• #362 Save annotations from bakta in subdirectories per sample. (by @jasmezz)
• #363 Removed warning from DeepBGC usage docs. (by @jasmezz)
• #365 Fixed AMRFinderPlus module and usage docs for manual database download. (by @jasmezz)
• #371 Fixed AMRFinderPlus parameter arg_amrfinderplus_name. (by @m3hdad)
• #377 Fixed an occasional RGI process failure when certain files not produced. (❤️ to @amizeranschi for reporting, fix by @amizeranschi & @jfy133)
• #386 Updated DeepBGC module to fix output file names, separate annotation step for all BGC tools, add warning if no BGCs found, fix MultiQC reporting of annotation workflow. (by @jfy133, @jasmezz)
• #393 & #397 Fixed a docker/singularity only error appearing when running with conda. (❤️ to @ewissel for reporting, fix by @jfy33 & @jasmezz)
• #391 Skip hmmmsearch by default to not crash pipeline if user provides no HMM files, updated docs. (by @jasmezz)
• #397 Removed deprecated AMPcombi module, fixed variable name in BGC workflow, updated minor parts in docs (usage, parameter schema). (by @jasmezz)
• #402 Fixed BGC length calculation for antiSMASH hits by comBGC. (by @jasmezz)
• #406 Fixed prediction tools not being executed if annotation workflow skipped. (by @jasmezz)
• #407 Fixed comBGC bug when parsing multiple antiSMASH files. (by @jasmezz)
• #409 Fixed argNorm overwriting its output for DeepARG. (by @jasmezz, @jfy133)
• #412 Improve all pre-run database download documentation. (by @jfy133)

Dependencies

Tool	Previous version	New version
AMPcombi	0.1.7	0.2.2
AMPlify	1.1.0	2.0.0
AMRFinderPlus	3.11.18	3.12.8
antiSMASH	6.1.1	7.1.0
argNorm	NA	0.5.0
bioawk	1.0	NA
comBGC	1.6.1	1.6.2
DeepARG	1.0.2	1.0.4
DeepBGC	0.1.30	0.1.31
GECCO	0.9.8	0.9.10
hAMRonization	1.1.1	1.1.4
HMMER	3.3.2	3.4
MMSeqs	NA	2:15.6f452
MultiQC	1.15	1.24
Pyrodigal	2.1.0	3.3.0
RGI	5.2.1	6.0.3
seqkit	NA	2.8.1
tabix/htslib	1.11	1.20

Deprecated

• #384 Deprecated AMPcombi and exchanged it with full suite of AMPcombi2 submodules. (by @Darcy220606)
• #382 Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. Bioawk is replaced with seqkit. (by @jfy133, @Darcy220606)

Photo by Victória Galina under CC BY-NC 3.0 BR

v1.1.6 - British Beans on Toast (Patch) - 2024-07-08

v1.1.6 - [2024-07-08]

Added

Fixed

• #396 Fixed bioawk overwriting input files. (❤️ to @Microbion for reporting, fix by @jfy133)

Dependencies

1.1.5 - British Beans on Toast (Patch) - 2024-03-20

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

1.1.4 - British Beans on Toast (Patch) - 2023-11-07

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

1.1.3 - British Beans on Toast (Patch) - 2023-08-11

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

1.1.2 - British Beans on Toast (Patch) - 2023-06-30

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

1.1.1 - British Beans on Toast (Patch) - 2023-04-27

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

1.1.0 - British Beans on Toast - 2023-04-27

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

Photo by Jon Chan under CC BY-SA 2.0

1.0.1 - German Rollmops (Patch) - 2023-02-27

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