Fix InterProScan ignoring staged database

CHANGELOG.md

@@ -14,6 +14,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#111](https://github.com/nf-core/proteinannotator/pull/111) - nf-core tools template update to 4.1.0. (by @vagkaratzas)
 - [#106](https://github.com/nf-core/proteinannotator/pull/106) - nf-core tools template update to 4.0.3. (by @vagkaratzas)
 
+### `Fixed`
+
+- [#115](https://github.com/nf-core/proteinannotator/pull/115) - Fixed `INTERPROSCAN` failing on real databases: updated the `interproscan` module so it uses the staged database ([nf-core/modules#13009](https://github.com/nf-core/modules/issues/13009)), set the default `interproscan_db_url` to the 5.59-91.0 release that matches the container, pass the inner `data/` directory of an untarred release to `INTERPROSCAN`, and removed `PIRSF` from the default `interproscan_applications`, since parallel samples can race to index its HMMs on a fresh database (see usage docs to re-enable it). (by @vagkaratzas)
+
 ### `Dependencies`
 
 | Tool   | Previous version | New version |

conf/test.config

@@ -31,7 +31,7 @@ params {
     metagroot_latest_link   = params.pipelines_testdata_base_path + 'proteinannotator/testdata/metagroot/metagroot_test.hmm.gz'
     // Functional annotation
     interproscan_db_url       = params.pipelines_testdata_base_path + 'proteinannotator/testdata/interproscan/interproscan_test.tar.gz'
-    interproscan_applications = 'Hamap,TIGRFAM,sfld'
+    interproscan_applications = 'TIGRFAM,sfld'
     kofamscan_profiles_url    = params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz'
     kofamscan_ko_list_url     = params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kofamscan/ko_list.gz'
 }

conf/test_full.config

@@ -23,7 +23,7 @@ params {
     metagroot_latest_link   = params.pipelines_testdata_base_path + 'proteinannotator/testdata/metagroot/metagroot_test.hmm.gz'
     // Functional annotation
     interproscan_db_url       = params.pipelines_testdata_base_path + 'proteinannotator/testdata/interproscan/interproscan_test.tar.gz'
-    interproscan_applications = 'Hamap,TIGRFAM,sfld'
+    interproscan_applications = 'TIGRFAM,sfld'
     kofamscan_profiles_url    = params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz'
     kofamscan_ko_list_url     = params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kofamscan/ko_list.gz'
 }

docs/output.md

@@ -128,7 +128,7 @@ Each of the `domain_annotation/` subfolders (e.g., `pfam`, `funfam`, `nmpfams`,
 </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 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. The default database applications that are used to functionally annotate sequences include
-Hamap, PANTHER, PIRSF, TIGRFAM and sfld, and are set through the `--interproscan_applications` parameter.
+Hamap, PANTHER, TIGRFAM and sfld, and are set through the `--interproscan_applications` parameter.
 
 See also [InterProScan output documentation](https://interproscan-docs.readthedocs.io/en/v5/), where most of these examples are taken from.
 

docs/usage.md

@@ -85,43 +85,44 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c
 [InterProScan](https://github.com/ebi-pf-team/interproscan) is used to provide more information about the proteins annotated on the contigs. By default, turning on this subworkflow without `--skip_interproscan` will download and unzip the InterPro database. The database will then be saved in the output directory `<output_directory>/downloaded_dbs/interproscan_db/`. We recommend keeping a copy of this directory for future reuse in case the results folder is deleted.
 
 > [!NOTE]
-> The large database download (5.5GB) can take up to 4 hours depending on the bandwidth.
+> The large database download (6.6GB) can take up to 4 hours depending on the bandwidth.
 
-A local version of the database can be supplied to the pipeline by passing the InterProScan database directory to `--interproscan_db <path/to/downloaded-untarred-interproscan_db-dir/>`. The directory can be created by running (e.g. for database version 5.72-103.0):
+The database release must match the InterProScan version in the pipeline's container, which is **5.59-91.0**. Newer releases rename or replace member databases (e.g. TIGRFAM was merged into NCBIfam) and will not be found.
 
-```
-curl -L https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz -o interproscan_db/interproscan-5.72-103.0-64-bit.tar.gz
-tar -xzf interproscan_db/interproscan-5.72-103.0-64-bit.tar.gz -C interproscan_db/
+A local version of the database can be supplied to the pipeline with `--interproscan_db`. This can be either the untarred release directory or the `data/` directory inside it. The directory can be created by running:
 
+```bash
+curl -L https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.59-91.0/interproscan-5.59-91.0-64-bit.tar.gz -o interproscan-5.59-91.0-64-bit.tar.gz
+tar -pxzf interproscan-5.59-91.0-64-bit.tar.gz
 ```
 
-The contents of the database directory should include the directory `data` in the top level with a number of subdirectories:
+This creates the following layout:
 
 ```
-interproscan_db/
-  └── data/
-    ├── antifam
-    ├── cdd
-    ├── funfam
-    ├── gene3d
-    ├── hamap
-    ├── ncbifam
-    ├── panther
-    | └── [18.0]
-    ├── pfam
-    | └── [36.0]
-    ├── phobius
-    ├── pirsf
-    ├── pirsr
-    ├── prints
-    ├── prosite
-    | └── [2023_05]
-    ├── sfld
-    ├── smart
-    ├── superfamily
-    └── tmhmm
+interproscan-5.59-91.0/          <- pass this (or its data/ subdirectory) to --interproscan_db
+  ├── bin/
+  ├── data/
+  │   ├── hamap/
+  │   ├── panther/
+  │   ├── pirsf/
+  │   ├── sfld/
+  │   ├── tigrfam/
+  │   └── ...
+  ├── interproscan.properties
+  ├── interproscan.sh
+  └── setup.py
 ```
 
+> [!NOTE]
+> The HMMs in the 5.59-91.0 release are not pre-indexed. The default applications do not need them indexed. PIRSF is not in the defaults because it indexes its own HMMs the first time it runs, and when several samples run InterProScan in parallel against a fresh database, they may all try to index the same PIRSF files at once. To add PIRSF to `--interproscan_applications`, index the database once before running the pipeline, from inside the untarred release directory (the one containing `setup.py` and `interproscan.properties`, not `data/`):
+>
+> ```bash
+> cd interproscan-5.59-91.0/
+> python3 setup.py -f interproscan.properties
+> ```
+>
+> For a database downloaded by the pipeline, run the same command inside `<output_directory>/downloaded_dbs/interproscan_db/`, then reuse that directory with `--interproscan_db`.
+
 ### KOfamScan
 
 [KOfamScan](https://github.com/takaram/kofam_scan) assigns KEGG Orthologs to protein sequences using the KOfam profile HMM database and KO-specific score thresholds. It runs by default and can be disabled with `--skip_kofamscan`.

modules.json

@@ -23,7 +23,7 @@
                     },
                     "interproscan": {
                         "branch": "master",
-                        "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
+                        "git_sha": "3137cddd6fa5fd47e1673081fa82a12644e91996",
                         "installed_by": ["modules"]
                     },
                     "kofamscan": {

nextflow.config

@@ -35,9 +35,9 @@ params {
 
     // Functional annotation
     skip_interproscan          = false
-    interproscan_db_url        = "https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz"
+    interproscan_db_url        = "https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.59-91.0/interproscan-5.59-91.0-64-bit.tar.gz"
     interproscan_db            = null
-    interproscan_applications  = 'Hamap,PANTHER,PIRSF,TIGRFAM,sfld'
+    interproscan_applications  = 'Hamap,PANTHER,TIGRFAM,sfld'
     interproscan_enableprecalc = false
     skip_kofamscan             = false
     kofamscan_profiles_url     = "https://www.genome.jp/ftp/db/kofam/profiles.tar.gz"

nextflow_schema.json

@@ -324,22 +324,22 @@
                 },
                 "interproscan_db_url": {
                     "type": "string",
-                    "default": "https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz",
-                    "help_text": "This allows the user to change the InterProScan database version that the pipeline will download for you automatically. To instead use a pre-downloaded database, please supply its path to `--interproscan_db`. Changing this URL allows for the use of the latest database release. By default this is set to `http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz`. ",
+                    "default": "https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.59-91.0/interproscan-5.59-91.0-64-bit.tar.gz",
+                    "help_text": "This allows the user to change the InterProScan database version that the pipeline will download for you automatically. To instead use a pre-downloaded database, please supply its path to `--interproscan_db`. The release must match the InterProScan version of the pipeline's container (5.59-91.0), so do not point this at a newer release. By default this is set to `https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.59-91.0/interproscan-5.59-91.0-64-bit.tar.gz`.",
                     "description": "Change the database version used for annotation.",
                     "fa_icon": "fas fa-database"
                 },
                 "interproscan_db": {
                     "type": "string",
-                    "help_text": "Use this to supply the path to a pre-downloaded InterProScan database. This can be any unzipped InterProScan version.\n\nFor more details on where to find different InterProScan databases see tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/UserDocs.html#obtaining-a-copy-of-interproscan).\n",
+                    "help_text": "Use this to supply the path to a pre-downloaded InterProScan database. This must be an untarred InterProScan 5.59-91.0 release, matching the pipeline's container. Either the release's top-level directory or its inner `data/` directory can be supplied.\n\nFor more details on where to find different InterProScan databases see tool [documentation](https://interproscan-docs.readthedocs.io/en/latest/UserDocs.html#obtaining-a-copy-of-interproscan).\n",
                     "description": "Path to pre-downloaded InterProScan database.",
                     "fa_icon": "fas fa-database"
                 },
                 "interproscan_applications": {
                     "type": "string",
-                    "default": "Hamap,PANTHER,PIRSF,TIGRFAM,sfld",
+                    "default": "Hamap,PANTHER,TIGRFAM,sfld",
                     "pattern": "^\\w+(,\\w+)*",
-                    "help_text": "A comma-separated string specifying the database(s) to be used to annotate the coding regions annotated during the contig annotation workflow of the pipeline. By default these include `Hamap,PANTHER,PIRSF,TIGRFAM,sfld`.\n\nFor more information about all possible databases see the tool [documentation](https://interproscan-docs.readthedocs.io/en/v5/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--applications`",
+                    "help_text": "A comma-separated string specifying the database(s) to be used to annotate the coding regions annotated during the contig annotation workflow of the pipeline. By default these include `Hamap,PANTHER,TIGRFAM,sfld`.\n\nFor more information about all possible databases see the tool [documentation](https://interproscan-docs.readthedocs.io/en/v5/HowToRun.html).\n\n> Modifies tool parameter(s):\n> - InterProScan: `--applications`",
                     "description": "Assigns the database(s) to be used to annotate the coding regions.",
                     "fa_icon": "fas fa-database"
                 },

subworkflows/local/functional_annotation/main.nf

@@ -36,6 +36,10 @@ workflow FUNCTIONAL_ANNOTATION {
                 .first()
         }
 
+        // A full release untars to the whole install; INTERPROSCAN needs its inner data/ folder
+        ch_interproscan_db = ch_interproscan_db
+            .map { database -> database.resolve('data').isDirectory() ? database.resolve('data') : database }
+
         INTERPROSCAN( ch_fasta, ch_interproscan_db )
         ch_interproscan_tsv = INTERPROSCAN.out.tsv
     }

subworkflows/local/functional_annotation/tests/nextflow.config

@@ -1,6 +1,6 @@
 process {
     withName: INTERPROSCAN {
-        ext.args = '--applications Hamap,TIGRFAM,sfld --disable-precalc'
+        ext.args = '--applications TIGRFAM,sfld --disable-precalc'
         memory   = 12.GB
         cpus     = 1
     }