Add InterProScan to Pipeline and integrate in AMPcombi #428
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.1.0. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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@nf-core-bot fix linting |
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@nf-core-bot fix linting |
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Also fixes issue number #434 |
jfy133
reviewed
Jan 10, 2025
| @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | |||
| - [#421](https://github.com/nf-core/funcscan/pull/421) Updated to nf-core template 3.0.2. (by @jfy133) | |||
| - [#427](https://github.com/nf-core/funcscan/pull/427) AMPcombi now can use multiple other databases for classifications. (by @darcy220606) | |||
| - [#429](https://github.com/nf-core/funcscan/pull/429) Updated to nf-core template 3.1.0. (by @jfy133 and @jasmezz) | |||
| - [#428](https://github.com/nf-core/funcscan/pull/XXX) Added InterProScan annotation workflow to the pipeline. The results are coupled to AMPcombi final table. (by @darcy220606) | |||
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Suggested change
| - [#428](https://github.com/nf-core/funcscan/pull/XXX) Added InterProScan annotation workflow to the pipeline. The results are coupled to AMPcombi final table. (by @darcy220606) | |
| - [#428](https://github.com/nf-core/funcscan/pull/428) Added InterProScan annotation workflow to the pipeline. The results are coupled to AMPcombi final table. (by @darcy220606) |
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| withName: INTERPROSCAN_DATABASE { | ||
| memory = { 6.GB * task.attempt } | ||
| time = { 4.h * task.attempt } // Download might take longer with some Bandwidth! |
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Suggested change
| time = { 4.h * task.attempt } // Download might take longer with some Bandwidth! | |
| time = { 4.h * task.attempt } |
| } | ||
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| withName: INTERPROSCAN { | ||
| ext.prefix = { "${meta.id}_interproscan.faa" } |
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Is this meant to have the file suffix at the end?
| @@ -676,7 +715,7 @@ process { | |||
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| withName: AMP_DATABASE_DOWNLOAD { | |||
| publishDir = [ | |||
| path: { "${params.outdir}/databases/${params.amp_ampcombi_db}" }, | |||
| path: { "${params.outdir}/databases/" }, | |||
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Suggested change
| path: { "${params.outdir}/databases/" }, | |
| path: { "${params.outdir}/databases/ampcombi" }, |
If we use the interproscan example above?
| @@ -25,6 +25,8 @@ results/ | |||
| | ├── prodigal/ | |||
| | ├── prokka/ | |||
| | └── pyrodigal/ | |||
| ├── function/ | |||
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What exactly do you mean here by function? I don't find that particularly descriptive and would'nt know what you mean by that necessarily.
| }, | ||
| "function_interproscan_disableresidueannottsv": { | ||
| "type": "boolean", | ||
| "help_text": "This disables the addition of the annotations assigned according to the databases activated to the final `<sample>_interproscan.tsv` file. Turning this ON will remove the annotations from the final table. We don't recommend turning this ON to ensure a successful run. \n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--enable-tsv-residue-annot`\n", |
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Suggested change
| "help_text": "This disables the addition of the annotations assigned according to the databases activated to the final `<sample>_interproscan.tsv` file. Turning this ON will remove the annotations from the final table. We don't recommend turning this ON to ensure a successful run. \n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--enable-tsv-residue-annot`\n", | |
| "help_text": "This disables the addition of the annotations assigned according to the databases activated to the final `<sample>_interproscan.tsv` file. Turning this on will remove the annotations from the final table. It is not recommended to use this option, as it likely will cause a run failure because xxxxxxxxxxxxxxxxxxx. \n\nFor more information about this flag see the tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--enable-tsv-residue-annot`\n", |
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| ch_ampcombi_complete = AMPCOMBI2_COMPLETE.out.tsv | ||
| if ( ch_summary_count == 0 || ch_summary_count == 1 ) { | ||
| log.warn("[nf-core/funcscan] AMPCOMBI2: ${ch_summary_count} file passed. Skipping AMPCOMBI2_COMPLETE, AMPCOMBI2_CLUSTER, and TAXONOMY MERGING steps.") |
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Suggested change
| log.warn("[nf-core/funcscan] AMPCOMBI2: ${ch_summary_count} file passed. Skipping AMPCOMBI2_COMPLETE, AMPCOMBI2_CLUSTER, and TAXONOMY MERGING steps.") | |
| log.warn("[nf-core/funcscan] AMPCOMBI2: ${ch_summary_count} file(s) passed. Skipping AMPCOMBI2_COMPLETE, AMPCOMBI2_CLUSTER, and TAXONOMY MERGING steps.") |
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It might be good (if not already) to describe in the output file that in some cases you may not get these output files if XYZ
| ch_interproscan_db = ( INTERPROSCAN_DATABASE.out.db ) | ||
| } | ||
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| INTERPROSCAN( ch_faa_for_interproscan, ch_interproscan_db ) |
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Missing versions mixing for interproscan
| INTERPROSCAN( ch_faa_for_interproscan, ch_interproscan_db ) | ||
| ch_interproscan_tsv = ch_interproscan_tsv.mix(INTERPROSCAN.out.tsv) | ||
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| // Current INTERPROSCAN version 5.59_91.0 only includes 13 columns and not 15 which ampcombi expects, so we added them here |
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What happens if INTERPROSCAN output changes 👀 this scares me slightly to hardcode this but I'm not familiar with either tool
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| ch_interproscan_tsv = FUNCTION.out.tsv.map { meta, file -> | ||
| if (file == [] || file.isEmpty()) { | ||
| log.warn("[nf-core/funcscan] Functional annotation with INTERPROSCAN produced an empty TSV file. Passing empty file for ${meta.id}.") |
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What does 'Passin'g mean here? Skipping?
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PR checklist
This PR adds InterProScan to FUNCSCAN. It also integrates it into AMPcombi v2.0.1, which can parse its output as an optional flag.
This PR also closes issue #434
🚨 🚨 As interproscan requires a large database, i have not added it to any of the CI tests as that would require 4 hours for just downloading the database!!!!
👀 👀 👀 👀 👀 👀 Still TODO once AMPcombi 2.0.1 is updated in nf-core: DONE!!
nf-core 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).