diff --git a/config/functional_annotation_modules.config b/config/functional_annotation_modules.config
index 0992ec3..51926cc 100644
--- 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
index 4608a7b..23f22fb 100644
--- 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
index f032637..4db56fb 100644
--- 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
deleted file mode 100644
index 099c608..0000000
--- a/modules/local/interproscan.nf
+++ /dev/null
@@ -1,34 +0,0 @@
-process INTERPROSCAN {
-    tag "${protein_fasta.baseName}"
-    label 'process_single'
-
-    conda "bioconda::interproscan=5.55_88.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/interproscan:5.55_88.0--hec16e2b_1':
-        'biocontainers/interproscan:5.55_88.0--hec16e2b_1' }"
-
-    input:
-    tuple val(meta), path(protein_fasta)
-
-    output:
-    tuple val(meta), path('*.tsv'), emit: tsv
-    path "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${protein_fasta.baseName}"
-    """
-    interproscan.sh \\
-        $args \\
-        -i $protein_fasta \\
-        -o ${prefix}.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        interproscan: \$( interproscan.sh --version | sed '1!d; s/.*version //' )
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/interproscan/environment.yml b/modules/nf-core/interproscan/environment.yml
new file mode 100644
index 0000000..36ec6fa
--- /dev/null
+++ b/modules/nf-core/interproscan/environment.yml
@@ -0,0 +1,7 @@
+name: interproscan
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::interproscan=5.59_91.0
diff --git a/modules/nf-core/interproscan/main.nf b/modules/nf-core/interproscan/main.nf
new file mode 100644
index 0000000..b22149b
--- /dev/null
+++ b/modules/nf-core/interproscan/main.nf
@@ -0,0 +1,88 @@
+process INTERPROSCAN {
+    tag "$meta.id"
+    label 'process_long'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/interproscan:5.59_91.0--hec16e2b_1' :
+        'biocontainers/interproscan:5.59_91.0--hec16e2b_1' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    val(out_ext)
+
+    output:
+    tuple val(meta), path('*.tsv') , optional: true, emit: tsv
+    tuple val(meta), path('*.xml') , optional: true, emit: xml
+    tuple val(meta), path('*.gff3'), optional: true, emit: gff3
+    tuple val(meta), path('*.json'), optional: true, emit: json
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_compressed = fasta.name.endsWith(".gz")
+    def fasta_name = fasta.name.replace(".gz", "")
+
+    def appl = "-appl TIGRFAM,FunFam,SFLD,PANTHER,Gene3D,Hamap,ProSiteProfiles,Coils,SMART,CDD,PRINTS,PIRSR,ProSitePatterns,AntiFam,Pfam,MobiDBLite"
+    if ( args.contains("-appl") ) {
+        appl = ""
+    }
+    switch ( out_ext ) {
+        case "tsv": break
+        case "xml": break
+        case "gff3": break
+        case "json": break
+        default:
+            out_ext = 'tsv';
+            log.warn("Unknown output file format provided (${out_ext}): selecting tsv as fallback");
+            break
+    }
+
+    //  -dp (disable precalculation) is on so no online dependency
+    """
+    if [ "${is_compressed}" == "true" ]; then
+        gzip -c -d ${fasta} > ${fasta_name}
+    fi
+
+    interproscan.sh \\
+        -cpu ${task.cpus} \\
+        -i ${fasta_name} \\
+        -f ${out_ext} \\
+        -dp \\
+        ${args} \\
+        ${appl} \\
+        -o ${prefix}.${out_ext}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+    interproscan: \$(echo \$(interproscan.sh --version 2>&1) | head -n 1 | sed 's/^.*InterProScan version//' | sed 's/\\s*InterProScan.*//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    switch ( out_ext ) {
+        case "tsv": break
+        case "xml": break
+        case "gff3": break
+        case "json": break
+        default:
+            out_ext = 'tsv';
+            log.warn("Unknown output file format provided (${out_ext}): selecting tsv as fallback");
+            break
+    }
+
+    """
+    touch ${prefix}.${out_ext}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        interproscan: \$(echo \$(interproscan.sh --version 2>&1) | head -n 1 | sed 's/^.*InterProScan version//' | sed 's/\\s*InterProScan.*//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/interproscan/meta.yml b/modules/nf-core/interproscan/meta.yml
new file mode 100644
index 0000000..e984bd3
--- /dev/null
+++ b/modules/nf-core/interproscan/meta.yml
@@ -0,0 +1,54 @@
+name: "interproscan"
+description: Produces protein annotations and predictions from an amino acids FASTA file
+keywords:
+  - annotation
+  - fasta
+  - interproscan
+tools:
+  - "interproscan":
+      description: "InterPro integrates together predictive information about proteins function from a number of partner resources"
+      homepage: "https://www.ebi.ac.uk/interpro/search/sequence/"
+      documentation: "https://interproscan-docs.readthedocs.io"
+      tool_dev_url: "https://github.com/ebi-pf-team/interproscan"
+      doi: "10.1093/bioinformatics/btu031"
+      licence: "['GPL v3']"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Input fasta file containing the amino acid query sequences
+      pattern: "*.{fa,fasta,fa.gz,fasta.gz}"
+  - out_ext:
+      type: string
+      description: Specify the type of output file to be generated
+      pattern: "tsv|xml|gff3|json"
+output:
+  - tsv:
+      type: file
+      description: Tab separated file containing with detailed hits
+      pattern: "*.{tsv}"
+  - xml:
+      type: file
+      description: XML file containing with detailed hits
+      pattern: "*.{xml}"
+  - gff3:
+      type: file
+      description: GFF3 file containing with detailed hits
+      pattern: "*.{gff3}"
+  - json:
+      type: file
+      description: JSON file containing with detailed hits
+      pattern: "*.{json}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@toniher"
+maintainers:
+  - "@toniher"
+  - "@vagkaratzas"
diff --git a/modules/nf-core/interproscan/tests/main.nf.test b/modules/nf-core/interproscan/tests/main.nf.test
new file mode 100644
index 0000000..7e77774
--- /dev/null
+++ b/modules/nf-core/interproscan/tests/main.nf.test
@@ -0,0 +1,65 @@
+nextflow_process {
+
+    name "Test Process INTERPROSCAN"
+    script "../main.nf"
+    process "INTERPROSCAN"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "interproscan"
+
+    test("Annotates set of input proteins in an output tsv file") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+                ]
+                input[1] = 'tsv'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.tsv).match("tsv") },
+                { assert process.out.versions }
+            )
+        }
+
+    }
+
+    test("Annotates set of zipped input proteins in an output xml file") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.test_data['sarscov2']['genome']['proteome_fasta_gz'], checkIfExists: true)
+                ]
+                input[1] = 'xml'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.xml).match("xml") },
+                { assert process.out.versions }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/interproscan/tests/main.nf.test.snap b/modules/nf-core/interproscan/tests/main.nf.test.snap
new file mode 100644
index 0000000..903b8c1
--- /dev/null
+++ b/modules/nf-core/interproscan/tests/main.nf.test.snap
@@ -0,0 +1,28 @@
+{
+    "tsv": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.tsv:md5,0e12562859bec64decc90e3dedd1a52e"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-01T11:58:56.075236858"
+    },
+    "xml": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.xml:md5,7a211c1a4761e2b9b8700e6e9abbb15f"
+                ]
+            ]
+        ],
+        "timestamp": "2023-11-01T12:29:19.50051319"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/interproscan/tests/nextflow.config b/modules/nf-core/interproscan/tests/nextflow.config
new file mode 100644
index 0000000..2043e2c
--- /dev/null
+++ b/modules/nf-core/interproscan/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: INTERPROSCAN {
+        ext.args = '-appl Coils'
+    }
+}
diff --git a/modules/nf-core/interproscan/tests/tags.yml b/modules/nf-core/interproscan/tests/tags.yml
new file mode 100644
index 0000000..ddb90f8
--- /dev/null
+++ b/modules/nf-core/interproscan/tests/tags.yml
@@ -0,0 +1,2 @@
+interproscan:
+  - modules/nf-core/interproscan/**
diff --git a/subworkflows/functional_annotation/README.md b/subworkflows/functional_annotation/README.md
index 134de19..fef2b10 100644
--- 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 +48,7 @@ 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'
     }
 }
 ```
diff --git a/subworkflows/functional_annotation/main.nf b/subworkflows/functional_annotation/main.nf
index 9073ae1..bf30c17 100644
--- a/subworkflows/functional_annotation/main.nf
+++ b/subworkflows/functional_annotation/main.nf
@@ -1,7 +1,7 @@
 include { BLAST_MAKEBLASTDB                                              } from "$projectDir/modules/nf-core/blast/makeblastdb/main"
 include { AGAT_EXTRACTSEQUENCES as GFF2PROTEIN                           } from "$projectDir/modules/local/agat/extractsequences"
 include { BLAST_BLASTP                                                   } from "$projectDir/modules/local/blast/blastp"
-include { INTERPROSCAN                                                   } from "$projectDir/modules/local/interproscan"
+include { INTERPROSCAN                                                   } from "$projectDir/modules/nf-core/interproscan"
 include { AGAT_MANAGEFUNCTIONALANNOTATION as MERGE_FUNCTIONAL_ANNOTATION } from "$projectDir/modules/local/agat/managefunctionalannotation"
 
 workflow FUNCTIONAL_ANNOTATION {
@@ -43,7 +43,10 @@ workflow FUNCTIONAL_ANNOTATION {
         GFF2PROTEIN.out.proteins.splitFasta( by: params.records_per_file, file: true ),
         blastdb_ch.map{ meta, db -> db }.collect()
     )
-    INTERPROSCAN( GFF2PROTEIN.out.proteins.splitFasta( by: params.records_per_file, file: true ) )
+    INTERPROSCAN( 
+        GFF2PROTEIN.out.proteins.splitFasta( by: params.records_per_file, file: true ),
+        'tsv'
+    )
     MERGE_FUNCTIONAL_ANNOTATION(
         gff_file,
         BLAST_BLASTP.out.txt.map{ meta, txt -> txt }.collectFile( name: 'blast_merged.tsv' ),