funcscan - 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

- Nextflow
Published by jasmezz about 1 year ago

funcscan - 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 'sampleid\tcontigid\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

- Nextflow
Published by jasmezz over 1 year ago

funcscan - 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

- Nextflow
Published by jfy133 almost 2 years ago

funcscan - 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

- Nextflow
Published by jasmezz about 2 years ago

funcscan - 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

- Nextflow
Published by jasmezz over 2 years ago

funcscan - 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

- Nextflow
Published by jasmezz almost 3 years ago

funcscan - 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

- Nextflow
Published by jfy133 almost 3 years ago

funcscan - 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

- Nextflow
Published by jasmezz about 3 years ago

funcscan - 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 ampcombicompletesummary.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](https://en.wikipedia.org/wiki/File:Beansonsourdoughtoast.jpg) by Jon Chan under CC BY-SA 2.0_

- Nextflow
Published by jasmezz about 3 years ago

funcscan - 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

- Nextflow
Published by jasmezz over 3 years ago

funcscan - 1.0.0 - German Rollmops - 2023-02-15

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](https://de.wikipedia.org/wiki/Rollmops#/media/Datei:Rollmops01retouched.jpg) by Ra Boe under CC BY-SA 2.5

- Nextflow
Published by jasmezz over 3 years ago