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
jfy133
reviewed
Jan 22, 2025
jasmezz
requested changes
Feb 4, 2025
| withName: SEQKIT_SEQ_FILTER { | ||
| ext.prefix = { "${meta.id}_cleaned.faa" } | ||
| publishDir = [ | ||
| path: { "${params.outdir}/protein_annotation/interproscan/" }, |
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Are we sure we want the output in ${params.outdir}/protein_annotation/interproscan/ and not in ${params.outdir}/annotation/interproscan/? I'd prefer the latter, to have it all in one place regardless of DNA (pyrodigal etc.) or protein annotation (interproscan). I think it's more intuitive to search for any annotation results in a single folder.
If not, what do you think of renaming the annotation output folder to contig_annotation?
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The other annotation tools in the annotation workflow are annotating CDS which also can be proteins. I would leave the annotation workflow as is because thats the baseline annotation step of the pipeline. This annotation step is more of an accessory annotation to the pipeline if the user wants more information from diff DB and (1) its technically not correct protein_annotation because those are nnot necessary proteins and (2) the plan is that we add more to this workflow (e.g. the functional annotation of those CDS) so protein annotation will no longer be valid.
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The ouput im not sure if its a good idea to add it in the same folder because those are two diff workflows
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Okay. No strong opinion from my side. I still don't find the naming super intuitive, but it can be. Or why not cds_annotation for the CDS tools (prokka etc.) versus protein_annotation (interproscan)?
| ch_versions = ch_versions.mix( INTERPROSCAN.out.versions ) | ||
| 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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Isn't this something to solve upstream on AMPcombi side? 😬 Is ok for now I guess, but better to have this column number check done by AMPcombi instead of pipeline level.
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And thats where updating the database version is not a good idea before testing.
AMPcombi was developed on an updated version of InterProScan to the one available as a nf-core module. So its rather updating the module on nf-core than downgrading AMPcombi.
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Okay! Fair point if AMPcombi is tested to work with a specific interproscan version 👍 Just need to remember to edit this code when interproscan nf-core module gets updated one day. We could do it 🤓
jasmezz
approved these changes
Feb 6, 2025
| "--applications ${params.protein_annotation_interproscan_applications}", | ||
| params.protein_annotation_interproscan_enableprecalc ? '' : '--disable-precalc', | ||
| params.protein_annotation_interproscan_enableresidueannot ? '' : '--disable-residue-annot', | ||
| params.protein_annotation_interproscan_disableresidueannottsv ? '--enable-tsv-residue-annot' : '', |
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Hmm no, I changed to enable it by default, i.e. if the param is false (which is default), then activate --enable-tsv-residue-annot. Or am I missing some logic of this?
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| curl -L https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.67-99.0/interproscan-5.67-99.0-64-bit.tar.gz -o interproscan_db/interproscan-5.67-99.0-64-bit.tar.gz | ||
| tar -xzf interproscan_db/interproscan-5.67-99.0-64-bit.tar.gz -C interproscan_db/ |
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No, I didn't. But you're right, then I will download it to our server and test it; would be nice to have a more recent version towards the pipeline release.
| }, | ||
| "protein_annotation_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. It is not recommended to use this option, as it will cause a run failure because the format of the resulting files will no longer be adequate for integration in the final summary tables. Currently, only applicable for AMPcombi2. \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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They cannot add it by ext.arg :D Everything that should be ext.arg is a pipeline parameter. If we don't offer it, the user cannot use it. That's why we add as much as necessary and leave out everything that shouldn't be touched (or is too irrelevant).
| ch_versions = ch_versions.mix( INTERPROSCAN.out.versions ) | ||
| 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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Okay! Fair point if AMPcombi is tested to work with a specific interproscan version 👍 Just need to remember to edit this code when interproscan nf-core module gets updated one day. We could do it 🤓
jasmezz
requested changes
Feb 6, 2025
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Things to do before merge:
- address the database update comments from my previous review since I tested the new interpro scan db version today (see comment here)
- either fix ampcombi/parsetables error as reported in AMP screening doesn't run when only a single tool is enabled #444 or outsource this to a different PR
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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).