Merge pull request #104 from MartinPippel/interproscan

Interproscan
NBISweden · Jan 12, 2024 · fef4301 · fef4301
2 parents f4aa59c + e368916
commit fef4301
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Showing 13 changed files with 310 additions and 95 deletions.
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/test.config b/config/test.config
@@ -29,12 +29,11 @@ if ( params.subworkflow == 'functional_annotation' ) {
     }
     process {
         withName: 'FUNCTIONAL_ANNOTATION:INTERPROSCAN' {
+            cpus = 2
             ext.args = [
-                '-f TSV',
                 // '--iprlookup',
                 // '--goterms', 
                 // '-pa', 
-                // '-dp', 
                 '-t p'
             ].join(' ').trim()
         }

diff --git a/modules.json b/modules.json
@@ -1,41 +1,58 @@
 {
-  "name": "NBIS Genome Annotation Workflow",
-  "homePage": "",
-  "repos": {
-    "https://github.com/nf-core/modules.git": {
-      "modules": {
-        "nf-core": {
-          "blast/makeblastdb": {
-            "branch": "master",
-            "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-            "installed_by": ["modules"],
-            "patch": "modules/nf-core/blast/makeblastdb/blast-makeblastdb.diff"
-          },
-          "busco": {
-            "branch": "master",
-            "git_sha": "6d6552cb582f56b6101c452e16ee7c23073f91de",
-            "installed_by": ["modules"]
-          },
-          "fastp": {
-            "branch": "master",
-            "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
-            "installed_by": ["modules"]
-          },
-          "fastqc": {
-            "branch": "master",
-            "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
-            "installed_by": ["modules"]
-          },
-          "multiqc": {
-            "branch": "master",
-            "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
-            "installed_by": ["modules"]
-          }
+    "name": "NBIS Genome Annotation Workflow",
+    "homePage": "",
+    "repos": {
+        "https://github.com/nf-core/modules.git": {
+            "modules": {
+                "nf-core": {
+                    "blast/makeblastdb": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": [
+                            "modules"
+                        ],
+                        "patch": "modules/nf-core/blast/makeblastdb/blast-makeblastdb.diff"
+                    },
+                    "busco": {
+                        "branch": "master",
+                        "git_sha": "6d6552cb582f56b6101c452e16ee7c23073f91de",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "fastp": {
+                        "branch": "master",
+                        "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "interproscan": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    }
+                }
+            },
+            "subworkflows": {
+                "nf-core": {}
+            }
         }
-      },
-      "subworkflows": {
-        "nf-core": {}
-      }
     }
-  }
 }
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