Add InterProScan to Pipeline and integrate in AMPcombi

CHANGELOG.md

@@ -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)
 
 ### `Fixed`
 
@@ -18,11 +19,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
-| Tool     | Previous version | New version |
-| -------- | ---------------- | ----------- |
-| AMPcombi | 0.2.2            | 2.0.1       |
-| Macrel   | 1.2.0            | 1.4.0       |
-| MultiQC  | 1.24.0           | 1.25.1      |
+| Tool         | Previous version | New version |
+| ------------ | ---------------- | ----------- |
+| AMPcombi     | 0.2.2            | 2.0.1       |
+| Macrel       | 1.2.0            | 1.4.0       |
+| MultiQC      | 1.24.0           | 1.25.1      |
+| InterProScan | -                | 5.59_91.0   |
 
 ### `Deprecated`
 

CITATIONS.md

@@ -70,6 +70,14 @@
 
   > 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)
 
+- [InterPro](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).
+
+- [InterProScan](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)
+
 - [Macrel](https://doi.org/10.7717/peerj.10555)
 
   > Santos-Júnior, C. D., Pan, S., Zhao, X. M., & Coelho, L. P. (2020). Macrel: antimicrobial peptide screening in genomes and metagenomes. PeerJ, 8, e10555. [DOI: 10.7717/peerj.10555](https://doi.org/10.7717/peerj.10555)

conf/base.config

@@ -230,4 +230,11 @@ process {
         memory = { 6.GB * task.attempt }
         time   = { 2.h * task.attempt }
     }
+
+    withName: INTERPROSCAN_DATABASE {
+        memory = { 6.GB * task.attempt }
+        time   = { 4.h * task.attempt } // Download might take longer with some Bandwidth!
+        cpus   = { 6 * task.attempt }
+    }
+
 }

conf/modules.config

@@ -83,7 +83,7 @@ process {
         ]
     }
 
-    withName: SEQKIT_SEQ {
+    withName: SEQKIT_SEQ_LENGTH {
         ext.prefix = { "${meta.id}_long" }
         publishDir = [
             path: { "${params.outdir}/bgc/seqkit/" },
@@ -96,6 +96,45 @@ process {
         ].join(' ').trim()
     }
 
+    withName: SEQKIT_SEQ_FILTER {
+        ext.prefix = { "${meta.id}_cleaned.faa" }
+        publishDir = [
+            path: { "${params.outdir}/function/interproscan/" },
+            mode: params.publish_dir_mode,
+            enabled: { params.run_function_interproscan },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+        ext.args   = [
+            "--gap-letters '* \t.' --remove-gaps"
+        ].join(' ').trim()
+    }
+
+    withName: INTERPROSCAN_DATABASE {
+        publishDir = [
+            path: { "${params.outdir}/databases/interproscan/" },
+            mode: params.publish_dir_mode,
+            enabled: params.save_db,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: INTERPROSCAN {
+        ext.prefix = { "${meta.id}_interproscan.faa" }
+        publishDir = [
+            path: { "${params.outdir}/function/interproscan/" },
+            mode: params.publish_dir_mode,
+            enabled: params.run_function_interproscan,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+        ext.args   = [
+            "--applications ${params.function_interproscan_applications}",
+            params.function_interproscan_enableprecalc ? '' : '--disable-precalc',
+            params.function_interproscan_enableresidueannot ? '' : '--disable-residue-annot',
+            params.function_interproscan_disableresidueannottsv ? '--enable-tsv-residue-annot' : '',
+            "--formats tsv"
+        ].join(' ').trim()
+    }
+
     withName: PROKKA {
         ext.prefix = { "${meta.id}_prokka" }
         publishDir = [
@@ -676,7 +715,7 @@ process {
 
     withName: AMP_DATABASE_DOWNLOAD {
         publishDir = [
-            path: { "${params.outdir}/databases/${params.amp_ampcombi_db}" },
+            path: { "${params.outdir}/databases/" },
             mode: params.publish_dir_mode,
             enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },

docs/output.md

@@ -25,6 +25,8 @@ results/
 |   ├── prodigal/
 |   ├── prokka/
 |   └── pyrodigal/
+├── function/
+|   └── interproscan/
 ├── amp/
 |   ├── ampir/
 |   ├── amplify/
@@ -74,6 +76,10 @@ ORF prediction and annotation with any of:
 - [Prokka](#prokka) – open reading frame prediction and functional protein annotation.
 - [Bakta](#bakta) – open reading frame prediction and functional protein annotation.
 
+CDS domain annotation:
+
+- [InterProScan](#interproscan) (default) – for open reading frame protein and domain predictions.
+
 Antimicrobial Resistance Genes (ARGs):
 
 - [ABRicate](#abricate) – antimicrobial resistance gene detection, based on alignment to one of several databases.
@@ -216,6 +222,23 @@ Output Summaries:
 
 [Bakta](https://github.com/oschwengers/bakta) is a tool for the rapid & standardised annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis. The output is used by some of the functional screening tools.
 
+### Functional classifications
+
+[InterProScan](#interproscan)
+
+#### InterProScan
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `interproscan/`
+  - `<samplename>_cleaned.faa`: clean version of the fasta files (amino acids) generated by one of the annotated tools. These contain sequences with no special character
+  - `<samplename>_interproscan_faa.tsv`: predicted proteins and domains using the InterPro database in TSV format
+
+</details>
+
+[InterProScan](https://academic.oup.com/bioinformatics/article/30/9/1236/237988?login=true) (**a**nti**m**icrobial **p**eptide **p**rediction **i**n **r**) was designed to predict the protein function and and provide possible domain and motif information for the coding regions. It utilizes the InterPro database that consists of multiple sister databases such as PANTHER, ProSite, Pfam, etc. More details can be found in the [documentation](https://interproscan-docs.readthedocs.io/en/latest/index.html).
+
 ### AMP detection tools
 
 [ampir](#ampir), [AMPlify](#amplify), [hmmsearch](#hmmsearch), [Macrel](#macrel)

docs/usage.md

@@ -111,7 +111,7 @@ We highly recommend performing quality control on input contigs before running t
 For example, ideally BGC screening requires contigs of at least 3,000 bp else downstream tools may crash.
 :::
 
-## Notes on screening tools and taxonomic classification
+## Notes on screening tools, taxonomic and functional classifications
 
 The implementation of some tools in the pipeline may have some particular behaviours that you should be aware of before you run the pipeline.
 
@@ -133,6 +133,18 @@ MMseqs2 is currently the only taxonomic classification tool used in the pipeline
   --taxa_classification_mmseqs_db_id 'Kalamari'
   ```
 
+### InterProScan
+
+[InterProScan](https://github.com/ebi-pf-team/interproscan) is currently the only functional classification tool that gives a snapshot of the protein families and domains for each coding region. By runnning this tool `--run_function_interproscan`, the [InterPro database](http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.67-99.0/) v5.67-99.0 is by default downloaded and prepared. This can be changed by downloading and extracting the files from any [InterPro version](http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/) and the path to the folder assigned.
+
+```bash
+--function_interproscan_db 'path/to/InterPro_directory/'
+```
+
+:::info
+By default the databases used to assign the nearest protein domain is set as `PANTHER,ProSiteProfiles,ProSitePatterns,Pfam`. An addition of other application to the list, does not guarantee that the results will be integrated correctly within `AMPcombi`.
+:::
+
 ### antiSMASH
 
 antiSMASH has a minimum contig parameter, in which only contigs of a certain length (or longer) will be screened. In cases where no hits are found in these, the tool ends successfully without hits. However if no contigs in an input file reach that minimum threshold, the tool will end with a 'failure' code, and cause the pipeline to crash.
@@ -258,6 +270,10 @@ The pipeline will automatically run Pyrodigal instead of Prodigal if the paramet
 This is due to an incompatibility issue of Prodigal's output `.gbk` file with multiple downstream tools.
 :::
 
+:::tip
+If the `run_function_interproscan` is activated, protein and domain classifications of the coding regions are generated and the output is then integrated into the `AMPcombi parsetables` resulting table for every sample and the complete summary files e.g., `Ampcombi_summary.tsv`.
+:::
+
 ### Abricate
 
 The default ABRicate installation comes with a series of 'default' databases:

modules.json

@@ -140,6 +140,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "interproscan": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "macrel/contigs": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

modules/local/interproscan_download.nf

@@ -0,0 +1,35 @@
+process INTERPROSCAN_DATABASE {
+    tag "interproscan_database_download"
+    label 'process_medium'
+
+    conda "conda-forge::sed=4.7"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/curl:7.80.0' :
+        'biocontainers/curl:7.80.0' }"
+
+    input:
+    val database_url
+
+    output:
+    path("interproscan_db/*")   , emit: db
+    path "versions.yml"         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    """
+    mkdir -p interproscan_db/
+
+    filename=\$(basename ${database_url})
+
+    curl -L ${database_url} -o interproscan_db/\$filename
+    tar -xzf interproscan_db/\$filename -C interproscan_db/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tar: \$(tar --version 2>&1 | sed -n '1s/tar (busybox) //p')
+        curl: "\$(curl --version 2>&1 | sed -n '1s/^curl \\([0-9.]*\\).*/\\1/p')"
+    END_VERSIONS
+    """
+}