Add BiG-SLiCE to BGC workflow (fresh branch)#529
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Things missing for you to address @SkyLexS, a couple of minor things but otherwise:
Note I simplified the modules.conf to rely on defaults on .nextflow.conf rather than trying to check within the configuration file manually.
Otherwise only one major thing that is missing:
- Adding BiG-SLiCE to the relevant test configs under
conf/and then in the.nf.testfiles under `
And then done!
| - **biosynthetic gene clusters** (tools: [antiSMASH](https://docs.antismash.secondarymetabolites.org), [DeepBGC](https://github.com/Merck/deepbgc), [GECCO](https://gecco.embl.de), [hmmsearch](http://hmmer.org) – summarised by [comBGC](#combgc)) | ||
| - **antibiotic resistance genes** (tools: [ABRicate](https://github.com/tseemann/abricate), [AMRFinderPlus](https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder), [DeepARG](https://bitbucket.org/gusphdproj/deeparg-ss/src/master), [fARGene](https://github.com/fannyhb/fargene), [RGI](https://card.mcmaster.ca/analyze/rgi) - summarised by [hAMRonization](https://github.com/pha4ge/hAMRonization). Results from ABRicate, AMRFinderPlus, and DeepARG are normalised to [ARO](https://obofoundry.org/ontology/aro.html) by [argNorm](https://github.com/BigDataBiology/argNorm).) | ||
| - **antimicrobial peptides** (tools: [Macrel](https://github.com/BigDataBiology/macrel), [AMPlify](https://github.com/bcgsc/AMPlify), [ampir](https://ampir.marine-omics.net), [hmmsearch](http://hmmer.org) - summarised by [AMPcombi](https://github.com/paleobiotechnology/AMPcombi)) | ||
| - **biosynthetic gene clusters** (tools: [antiSMASH](https://docs.antismash.secondarymetabolites.org), [DeepBGC](https://github.com/Merck/deepbgc), [GECCO](https://gecco.embl.de), [hmmsearch](http://hmmer.org), [BiGSLiCE](https://github.com/medema-group/bigslice), - summarised by [comBGC](#combgc)) |
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| - **biosynthetic gene clusters** (tools: [antiSMASH](https://docs.antismash.secondarymetabolites.org), [DeepBGC](https://github.com/Merck/deepbgc), [GECCO](https://gecco.embl.de), [hmmsearch](http://hmmer.org), [BiGSLiCE](https://github.com/medema-group/bigslice), - summarised by [comBGC](#combgc)) | |
| - **biosynthetic gene clusters** (tools: [antiSMASH](https://docs.antismash.secondarymetabolites.org), [DeepBGC](https://github.com/Merck/deepbgc), [GECCO](https://gecco.embl.de), [hmmsearch](http://hmmer.org), [BiGSLiCE](https://github.com/medema-group/bigslice) - summarised by [comBGC](#combgc)) |
| - [#507](https://github.com/nf-core/funcscan/pull/507) Updated to nf-core template v3.5.1 (by @jfy133) | ||
| - [#510](https://github.com/nf-core funcscan/pull/510) Fixed code to make Nextflow strict-syntax compliant (by @jfy133) | ||
| - [#521](https://github.com/nf-core funcscan/pull/521) Added option to turn on RGI's own cleanup of intermediate files (❤️ to @SamD28 for requesting, added by @jfy133) | ||
| - [#519](https://github.com/nf-core/funcscan/pull/519) Added BiG-SLiCE (`bigslice`) as a new BGC clustering tool in the BGC subworkflow. Activated with `--bgc_run_bigslice` and requires `--bgc_bigslice_db`. (by @SkyLexS) |
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| - [#519](https://github.com/nf-core/funcscan/pull/519) Added BiG-SLiCE (`bigslice`) as a new BGC clustering tool in the BGC subworkflow. Activated with `--bgc_run_bigslice` and requires `--bgc_bigslice_db`. (by @SkyLexS) | |
| - [#519](https://github.com/nf-core/funcscan/pull/519) Added BiG-SLiCE (`bigslice`) as a new BGC clustering tool in the BGC subworkflow. Activated with `--bgc_run_bigslice` and requires `--bgc_bigslice_db` (by @SkyLexS) |
| | dbCAN | | 5.2.9 | | ||
| | MultiQC | 1.27 | 1.34 | | ||
| | Bakta | 1.10.4 | 1.11.4 | | ||
| | BiG-SLiCE | | 2.0.2 | |
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| | BiG-SLiCE | | 2.0.2 | | |
| | BiG-SLiCE | | 2.0.2 | | |
| | nf-core | 3.3.2 | 4.0.2 | |
| bgc_bigslice_complete = false | ||
| bgc_bigslice_export_tsv = false | ||
| bgc_bigslice_threshold = 0.4 | ||
| bgc_bigslice_threshold_pct = 0.0 |
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| bgc_bigslice_threshold_pct = 0.0 | |
| bgc_bigslice_threshold_pct = -1 |
To match the default
--threshold_pct Calculate clustering threshold (T) based on a random sampling of pairwise distances between the data, taking the N-th percentile value as the threshold. Mutually exclusive with --threshold, use '-1' to turn off this parameter (default: -1).
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| bgc_bigslice_export_tsv = false | ||
| bgc_bigslice_threshold = 0.4 | ||
| bgc_bigslice_threshold_pct = 0.0 | ||
| bgc_bigslice_n_ranks = 1 |
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| bgc_bigslice_export_tsv = false | |
| bgc_bigslice_threshold = 0.4 | |
| bgc_bigslice_threshold_pct = 0.0 | |
| bgc_bigslice_n_ranks = 1 | |
| bgc_bigslice_exporttsv = false | |
| bgc_bigslice_threshold = 0.4 | |
| bgc_bigslice_thresholdpct = 0.0 | |
| bgc_bigslice_nranks = 1 |
Make sure to update names everywhere used in the codee
| .collect() | ||
| .map { files -> [[id: 'bigslice'], files.flatten()] } | ||
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| BIGSLICE_DOWNLOADDB([id: 'bigslice_db']) |
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This should only happen if --bgc_bigslice_db is not supplied, right? Please add a condition and an additional input channel for when it has been supplied
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I was wondering if i should still keep the manual option, but in the end I think its a good idea to have them both
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Yes we should always keep the manual option, because people on offline clusters can't have pipeline download stuff for them
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Re-do of #519 but on a fresh branch due a faulty Git merge, but with a fixed module structure for bigslice
All this work was originally done by @SkyLexS
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).