NBISweden · MartinPippel · Jan 12, 2024 · Jan 11, 2024 · Jan 11, 2024 · Jan 11, 2024
diff --git a/config/functional_annotation_modules.config b/config/functional_annotation_modules.config
@@ -17,11 +17,9 @@ process {
     }
     withName: 'INTERPROSCAN' {
         ext.args = [
-            '-f TSV',
             '--iprlookup',
             '--goterms', 
             '-pa', 
-            '-dp', 
             '-t p'
         ].join(' ').trim()
     }

diff --git a/config/nf-core-defaults.config b/config/nf-core-defaults.config
@@ -29,6 +29,7 @@ process {
     }
     withLabel: process_long {
         time   = 20.h
+        cpus   = 4
     }
     withLabel: process_high_memory {
         memory = 120.GB

diff --git a/config/test.config b/config/test.config
@@ -30,12 +30,13 @@ if ( params.subworkflow == 'functional_annotation' ) {
     process {
         withName: 'FUNCTIONAL_ANNOTATION:INTERPROSCAN' {
             ext.args = [
-                '-f TSV',
+                //'-f TSV',
                 // '--iprlookup',
                 // '--goterms', 
                 // '-pa', 
                 // '-dp', 
                 '-t p'
+
             ].join(' ').trim()
         }
     }
@@ -77,6 +78,7 @@ process {
     }
     withLabel: process_long {
         time   = 1.h
+        cpus   = 2
     }
     withLabel: process_high_memory {
         memory = 6.GB

diff --git a/modules.json b/modules.json
@@ -26,6 +26,11 @@
             "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
             "installed_by": ["modules"]
           },
+          "interproscan": {
+            "branch": "master",
+            "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+            "installed_by": ["modules"]
+          },
           "multiqc": {
             "branch": "master",
             "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",

diff --git a/modules/local/interproscan.nf b/modules/local/interproscan.nf
diff --git a/modules/nf-core/interproscan/environment.yml b/modules/nf-core/interproscan/environment.yml
diff --git a/modules/nf-core/interproscan/main.nf b/modules/nf-core/interproscan/main.nf
diff --git a/modules/nf-core/interproscan/meta.yml b/modules/nf-core/interproscan/meta.yml
diff --git a/modules/nf-core/interproscan/tests/main.nf.test b/modules/nf-core/interproscan/tests/main.nf.test
diff --git a/modules/nf-core/interproscan/tests/main.nf.test.snap b/modules/nf-core/interproscan/tests/main.nf.test.snap
diff --git a/modules/nf-core/interproscan/tests/nextflow.config b/modules/nf-core/interproscan/tests/nextflow.config
diff --git a/modules/nf-core/interproscan/tests/tags.yml b/modules/nf-core/interproscan/tests/tags.yml
diff --git a/subworkflows/functional_annotation/README.md b/subworkflows/functional_annotation/README.md
@@ -26,23 +26,6 @@ nextflow run NBISweden/pipelines-nextflow \
     -params-file params.yml
 ```
 
-> **note**
->
-> The Interproscan conda package is temperamental. Please use a local installation
-> by overriding the workflow configuration.
->
-> `nextflow.config`:
->
-> ```nextflow
-> process {
->     withName: 'INTERPROSCAN' {
->         conda = null
->         container = null
->         module = 'bioinfo-tools:InterProScan/5.30-69.0'  // Load Uppmax modules `bioinfo-tools` and `InterProScan/5.30-69.0`
->     }    
-> }
-> ```
-
 ## Parameters
 
 - General:
@@ -65,7 +48,8 @@ These command line tool parameters can be changed by overriding the `ext.args` v
 ```nextflow
 process {
     withName: 'INTERPROSCAN' {
-        ext.args = '-f TSV --iprlookup --goterms -pa -dp -t p'
+        //
+        ext.args = '--iprlookup --goterms -pa -t p'
     }
 }
 ```