output.md updated

Author: vagkaratzas

CHANGELOG.md

@@ -9,6 +9,7 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https://
 
 ### `Added`
 
+- [#67](https://github.com/nf-core/proteinannotator/pull/67) - Swapped to the updated, non-buggy, nf-core version of `INTERPROSCAN`. (by @vagkaratzas)
 - [#65](https://github.com/nf-core/proteinannotator/pull/65) - Converted the pipeline schematic to nf-core metromap. (by @vagkaratzas)
 - [#62](https://github.com/nf-core/proteinannotator/pull/62) - Added the option to download and use the latest FunFam HMM library (or use path to an existing one) for domain annotation. (by @vagkaratzas)
 - [#61](https://github.com/nf-core/proteinannotator/pull/61) - Added nf-core modules `ARIA2` and `HMMER_HMMSEARCH` to download latest Pfam HMM library (or use path to existing one) and match domains to input sequences. (by @vagkaratzas)

conf/modules.config

@@ -120,7 +120,7 @@ process {
 
     withName: 'NFCORE_PROTEINANNOTATOR:PROTEINANNOTATOR:FUNCTIONAL_ANNOTATION:INTERPROSCAN' {
         publishDir = [
-            path: { "${params.outdir}/functional_annotation/interproscan/" },
+            path: { "${params.outdir}/functional_annotation/interproscan/${meta.id}/" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]

docs/output.md

@@ -103,15 +103,23 @@ Each of the `domain_annotation/` subfolders (e.g., `pfam`, `funfam`) contain a `
 <details markdown="1">
 <summary>Output files</summary>
 
-- `functional_annotation/interproscan`
-  - `*.gff.gz`: gzip-compressed general feature format (GFF) file
-  - `*.json.gz`: gzip-compressed javascript object notation (JSON) file
-  - `*.tsv.gz`: gzip-compressed tab-separated variable (TSV) file
-  - `*.xml.gz`: gzip-compressed eXtensible markup language (XML) file
+- `downloaded_dbs/`
+  - `data/`: (optional) uncompressed archive data from the downloaded InterProScan database
+    - `*/`: (optional) one directory for each of the member databases of InterProScan
+  - `interproscan_test.tar.gz`: (optional) the downloaded InterProScan archive of member databases according to the optional user-provided url
+- `functional_annotation/`
+  - `interproscan/`
+    - `<samplename>/`
+      - `<samplename>.gff`: general feature format (GFF) file
+      - `<samplename>.json`: javascript object notation (JSON) file
+      - `<samplename>.tsv`: tab-separated variable (TSV) file
+      - `<samplename>.xml`: eXtensible markup language (XML) file
 
 </details>
 
-[InterProScan](https://interproscan-docs.readthedocs.io/en/v5/#) is a protein annotation tool that searches [InterPro](http://www.ebi.ac.uk/interpro/), a database which integrates together predictive information about proteins’ function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains.
+[InterProScan](https://interproscan-docs.readthedocs.io/en/v5/#) is a protein annotation tool that searches [InterPro](http://www.ebi.ac.uk/interpro/), a database which integrates predictive information about protein function from a number of member resources, giving an overview of the families that a protein belongs to and the domains and sites it contains.
+For `nf-core/proteinannotator`, the default database applications that are used to functionally annotate sequences include
+Hamap, PANTHER, PIRSF, TIGRFAM and sfld. The main `nextflow.config` contains a [url]("https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz") parameter (`--interproscan_db_url`) for the full version of the InterProScan database, whereas the test profiles override that with a minimal test version of the database. If, instead, a local database is provided via the `--interproscan_db` parameter, then the download is skipped.
 
 See also [InterProScan output documentation](https://interproscan-docs.readthedocs.io/en/v5/), where most of these examples are taken from.