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
| | MultiQC | 1.24.0 | 1.27 | | ||
| | Pyrodigal | 3.3.0 | 3.6.3 | | ||
| | seqkit | 2.8.1 | 2.9.0 | | ||
| ======= |
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| | 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 | |
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Is this table formatting intended? I don't know if we should write it like this (i.e. without filling up spaces).
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| > Eddy S. R. (2011). Accelerated Profile HMM Searches. PLoS computational biology, 7(10), e1002195. [DOI: 10.1371/journal.pcbi.1002195](https://doi.org/10.1371/journal.pcbi.1002195) | |||
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| - [InterPro](https://doi.org/10.1093/nar/gkaa977) | |||
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| > Blum, M., Chang, H-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., Richardson, L., Salazar, G.A., Williams, L., Bork, P., Bridge, A., Gough, J., Haft, D.H., Letunic, I., Marchler-Bauer, A., Mi, H., Natale, D.A., Necci, M., Orengo, C.A., Pandurangan, A.P., Rivoire, C., Sigrist, C.A., Sillitoe, I., Thanki, N., Thomas, P.D., Tosatto, S.C.E, Wu, C.H., Bateman, A., Finn, R.D. (2021) The InterPro protein families and domains database: 20 years on, Nucleic Acids Research, 49(D1), D344–D354.[DOI: 10.1093/nar/gkaa977](https://doi.org/10.1093/nar/gkaa977). | |||
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Suggested change
| > Blum, M., Chang, H-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., Richardson, L., Salazar, G.A., Williams, L., Bork, P., Bridge, A., Gough, J., Haft, D.H., Letunic, I., Marchler-Bauer, A., Mi, H., Natale, D.A., Necci, M., Orengo, C.A., Pandurangan, A.P., Rivoire, C., Sigrist, C.A., Sillitoe, I., Thanki, N., Thomas, P.D., Tosatto, S.C.E, Wu, C.H., Bateman, A., Finn, R.D. (2021) The InterPro protein families and domains database: 20 years on, Nucleic Acids Research, 49(D1), D344–D354.[DOI: 10.1093/nar/gkaa977](https://doi.org/10.1093/nar/gkaa977). | |
| > Blum, M., Chang, H-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., Richardson, L., Salazar, G. A., Williams, L., Bork, P., Bridge, A., Gough, J., Haft, D. H., Letunic, I., Marchler-Bauer, A., Mi, H., Natale, D. A., Necci, M., Orengo, C. A., Pandurangan, A. P., Rivoire, C., Sigrist, C. A., Sillitoe, I., Thanki, N., Thomas, P. D., Tosatto, S. C. E, Wu, C. H., Bateman, A., Finn, R. D. (2021) The InterPro protein families and domains database: 20 years on. Nucleic Acids Research, 49(D1), D344–D354. [DOI: 10.1093/nar/gkaa977](https://doi.org/10.1093/nar/gkaa977) |
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| - [InterProScan](https://doi.org/10.1093/bioinformatics/btu031) | ||
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| > Jones, P., Binns, D., Chang, H-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A.F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S-Y., Lopez, R., Hunter, S. (2014)InterProScan 5: genome-scale protein function classification, Bioinformatics, 30(9), 1236–1240. [DOI: 10.1093/bioinformatics/btu031](https://doi.org/10.1093/bioinformatics/btu031) |
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| > Jones, P., Binns, D., Chang, H-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A.F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S-Y., Lopez, R., Hunter, S. (2014)InterProScan 5: genome-scale protein function classification, Bioinformatics, 30(9), 1236–1240. [DOI: 10.1093/bioinformatics/btu031](https://doi.org/10.1093/bioinformatics/btu031) | |
| > Jones, P., Binns, D., Chang, H-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A. F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S-Y., Lopez, R., Hunter, S. (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics, 30(9), 1236–1240. [DOI: 10.1093/bioinformatics/btu031](https://doi.org/10.1093/bioinformatics/btu031) |
| 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?
| .first() | ||
| } else { | ||
| INTERPROSCAN_DATABASE ( params.protein_annotation_interproscan_db_url ) | ||
| ch_versions = ch_versions.mix( INTERPROSCAN_DATABASE.out.versions ) |
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| ch_versions = ch_versions.mix( INTERPROSCAN_DATABASE.out.versions ) | |
| ch_versions = ch_versions.mix( INTERPROSCAN_DATABASE.out.versions ) |
| } | ||
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| INTERPROSCAN( ch_faa_for_interproscan, ch_interproscan_db ) | ||
| ch_versions = ch_versions.mix( INTERPROSCAN.out.versions ) |
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| ch_versions = ch_versions.mix( INTERPROSCAN.out.versions ) | |
| ch_versions = ch_versions.mix( INTERPROSCAN.out.versions ) |
| 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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| PROTEIN_ANNOTATION ( | ||
| ch_input_for_protein_annotation | ||
| ) |
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| PROTEIN_ANNOTATION ( | |
| ch_input_for_protein_annotation | |
| ) | |
| PROTEIN_ANNOTATION ( ch_input_for_protein_annotation ) |
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| ch_interproscan_tsv = PROTEIN_ANNOTATION.out.tsv.map { meta, file -> | ||
| if (file == [] || file.isEmpty()) { | ||
| log.warn("[nf-core/funcscan] Protein annotation with INTERPROSCAN produced an empty TSV file. No protein annotation will be added for ${meta.id}.") |
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Suggested change
| log.warn("[nf-core/funcscan] Protein annotation with INTERPROSCAN produced an empty TSV file. No protein annotation will be added for ${meta.id}.") | |
| log.warn("[nf-core/funcscan] Protein annotation with InterProScan produced an empty TSV file. No protein annotation will be added for sample ${meta.id}.") |
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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).