Repository: nf-core/rnafusion
Pull request #650: update fusioncatcher to nf-core
Author: login: nvnieuwk
Created: 2025-04-11T09:56:01Z | Merged: 2025-04-22T09:51:05Z

This should hopefully fix the issues encountered with the fusioncatcher build process. I'm currently running a test for this.


Diff:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f5dae60d6..ce6860041 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - `crai`: The index of the CRAM file, this is not required when a `cram` file has been given but can increase the pipeline speed a bit.
   - `junctions`: A file containing the junctions determined by STAR (needed by `starfusion` and `ctatsplicing`)
   - `splice_junctions` A file containing the splice junctions determined by STAR (needed by `ctatsplicing`)
+- Added `--fusioncatcher_download_link`. [#650](https://github.com/nf-core/rnafusion/pull/650)
 
 ### Changed
 
@@ -93,13 +94,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Remove fusionGDB from documentation and fusion-report download stubs [#503](https://github.com/nf-core/rnafusion/pull/503)
 - Removed test-build as reference building gets integrated in the main workflow [#505](https://github.com/nf-core/rnafusion/pull/505)
 - Removed parameter `--build_references`
+- Removed fusioncatcher build [#650](https://github.com/nf-core/rnafusion/pull/650)
 
 ### Parameters
 
-| Old parameter        | New parameter       |
-| -------------------- | ------------------- |
-|                      | `--no_cosmic`       |
-| `--build_references` | `--references_only` |
+| Old parameter         | New parameter                   |
+| --------------------- | ------------------------------- |
+|                       | `--no_cosmic`                   |
+| `--build_references`  | `--references_only`             |
+| `--fastp_trim`        | `--tools fastp`                 |
+| `--arriba`            | `--tools arriba`                |
+| `--run_fusioncatcher` | `--tools fusioncatcher`         |
+| `--starfusion`        | `--tools starfusion`            |
+| `--stringtie`         | `--tools stringtie`             |
+| `--all`               | `--tools all`                   |
+|                       | `--fusioncatcher_download_link` |
 
 ## v3.0.2 - [2024-04-10]
 
diff --git a/conf/modules.config b/conf/modules.config
index 67b73e49a..b9cf58749 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -87,8 +87,12 @@ process {
         ]
     }
 
-    withName: 'FUSIONCATCHER' {
-        ext.args = "--limitSjdbInsertNsj ${params.fusioncatcher_limitSjdbInsertNsj}"
+    withName: 'FUSIONCATCHER_FUSIONCATCHER' {
+        ext.args = {[
+            "--limitSjdbInsertNsj ${params.fusioncatcher_limitSjdbInsertNsj}",
+            "--skip-blat",
+            meta.single_end ? "--single-end" : "",
+        ].join(' ')}
     }
 
     withName: 'FUSIONCATCHER_DOWNLOAD' {
diff --git a/modules.json b/modules.json
index a0547e179..04fcccc52 100644
--- a/modules.json
+++ b/modules.json
@@ -40,6 +40,11 @@
                         "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
+                    "fusioncatcher/fusioncatcher": {
+                        "branch": "master",
+                        "git_sha": "2a227f75f33415f74a884ef8b33555b151e33de9",
+                        "installed_by": ["modules"]
+                    },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
                         "git_sha": "1999eff2c530b2b185a25cc42117a1686f09b685",
diff --git a/modules/local/fusioncatcher/build/environment.yml b/modules/local/fusioncatcher/build/environment.yml
deleted file mode 100644
index 8e83de36b..000000000
--- a/modules/local/fusioncatcher/build/environment.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bioconda::fusioncatcher=1.33
diff --git a/modules/local/fusioncatcher/build/main.nf b/modules/local/fusioncatcher/build/main.nf
deleted file mode 100644
index db1c72107..000000000
--- a/modules/local/fusioncatcher/build/main.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-process FUSIONCATCHER_BUILD {
-    tag "fusioncatcher_build"
-    label 'process_medium'
-
-    conda "${projectDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' :
-        'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }"
-
-    input:
-    val genome_gencode_version
-
-    output:
-    tuple env(meta), path("human_v${genome_gencode_version}"), emit: reference
-    path "versions.yml"                                      , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-
-    def args = task.ext.args ?: ''
-    meta = [ id: "human_v${genome_gencode_version}" ]
-    """
-    fusioncatcher-build.py \\
-        -g homo_sapiens \\
-        -o human_v${genome_gencode_version} \\
-        $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
-    END_VERSIONS
-    """
-
-    stub:
-    """
-    mkdir human_v${genome_gencode_version}
-    touch human_v${genome_gencode_version}/ensembl_fully_overlapping_genes.txt
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/fusioncatcher/build/meta.yml b/modules/local/fusioncatcher/build/meta.yml
deleted file mode 100644
index 202be7e17..000000000
--- a/modules/local/fusioncatcher/build/meta.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-name: fusioncatcher_build
-description: Build genome for fusioncatcher
-keywords:
-  - sort
-tools:
-  - fusioncatcher:
-      description: Build genome for fusioncatcher
-      homepage: https://github.com/ndaniel/fusioncatcher/
-      documentation: https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md
-      tool_dev_url: https://github.com/ndaniel/fusioncatcher/
-      doi: "10.1101/011650"
-      licence: ["GPL v3"]
-
-output:
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - reference:
-      type: directory
-      description: Path to fusioncatcher references
-
-authors:
-  - "@praveenraj2018, @rannick"
diff --git a/modules/local/fusioncatcher/detect/environment.yml b/modules/local/fusioncatcher/detect/environment.yml
deleted file mode 100644
index 8e83de36b..000000000
--- a/modules/local/fusioncatcher/detect/environment.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bioconda::fusioncatcher=1.33
diff --git a/modules/local/fusioncatcher/detect/main.nf b/modules/local/fusioncatcher/detect/main.nf
deleted file mode 100644
index 7980439f8..000000000
--- a/modules/local/fusioncatcher/detect/main.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-process FUSIONCATCHER_DETECT {
-    tag "$meta.id"
-    label 'process_high'
-
-    conda "${projectDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' :
-        'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }"
-
-    input:
-    tuple val(meta), path(fastqs, stageAs: "input/*")
-    tuple val(meta2), path(reference)
-
-    output:
-    tuple val(meta), path("*.fusioncatcher.fusion-genes.txt"), emit: fusions, optional: true
-    tuple val(meta), path("*.fusioncatcher.summary.txt")     , emit: summary, optional: true
-    tuple val(meta), path("*.fusioncatcher.log")             , emit: log
-    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 single_end = meta.single_end ? "--single-end" : ""
-    """
-    fusioncatcher.py \\
-        -d ${reference} \\
-        -i input \\
-        -p ${task.cpus} \\
-        -o . \\
-        --skip-blat \\
-        ${single_end} \\
-        ${args}
-
-    mv final-list_candidate-fusion-genes.txt ${prefix}.fusioncatcher.fusion-genes.txt
-    mv summary_candidate_fusions.txt ${prefix}.fusioncatcher.summary.txt
-    mv fusioncatcher.log ${prefix}.fusioncatcher.log
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fusioncatcher: "\$(fusioncatcher.py --version 2>&1 | awk '{print \$2}')"
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    """
-    touch ${prefix}.fusioncatcher.fusion-genes.txt
-    touch ${prefix}.fusioncatcher.summary.txt
-    touch ${prefix}.fusioncatcher.log
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fusioncatcher: "\$(fusioncatcher.py --version 2>&1 | awk '{print \$2}')"
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/fusioncatcher/detect/meta.yml b/modules/local/fusioncatcher/detect/meta.yml
deleted file mode 100644
index 7c8ee425a..000000000
--- a/modules/local/fusioncatcher/detect/meta.yml
+++ /dev/null
@@ -1,53 +0,0 @@
-name: fusioncatcher
-description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
-keywords:
-  - fusioncatcher
-tools:
-  - fusioncatcher:
-      description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
-      homepage: https://github.com/ndaniel/fusioncatcher
-      documentation: https://github.com/ndaniel/fusioncatcher/wiki
-      tool_dev_url: https://github.com/ndaniel/fusioncatcher
-      doi: "10.1101/011650v1"
-      licence: ["GPL v3"]
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: FASTQ file
-      pattern: "*.{fastq}"
-  - reference:
-      type: directory
-      description: Path to fusioncatcher references
-      pattern: "*"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - fusions:
-      type: file
-      description: Final list of candidate fusion genes
-      pattern: "*.fusioncatcher.fusion-genes.txt"
-  - summary:
-      type: file
-      description: Summary of fusion results
-      pattern: "*.fusioncatcher_summary.txt"
-  - log:
-      type: file
-      description: Log of fusion results
-      pattern: "*.fusioncatcher.log"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@praveenraj2018. @rannick"
diff --git a/modules/local/fusioncatcher/download/main.nf b/modules/local/fusioncatcher/download/main.nf
index af585d62c..f2cc2a3d5 100644
--- a/modules/local/fusioncatcher/download/main.nf
+++ b/modules/local/fusioncatcher/download/main.nf
@@ -2,17 +2,17 @@ process FUSIONCATCHER_DOWNLOAD {
     tag "fusioncatcher_download"
     label 'process_medium'
 
-    conda "${projectDir}/environment.yml"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' :
-        'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3b/3b54fa9135194c72a18d00db6b399c03248103f87e43ca75e4b50d61179994b3/data':
+        'community.wave.seqera.io/library/wget:1.21.4--8b0fcde81c17be5e' }"
 
     input:
     val genome_gencode_version
 
     output:
-    tuple env(meta), path("*"), emit: reference
-    path "versions.yml"       , emit: versions
+    tuple env(meta), path("human_v*"), emit: reference
+    path "versions.yml"              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,16 +22,16 @@ process FUSIONCATCHER_DOWNLOAD {
     def args = task.ext.args ?: ''
     meta = [ id: "human_v${genome_gencode_version}" ]
     """
-    wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${genome_gencode_version}.tar.gz.aa
-    wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${genome_gencode_version}.tar.gz.ab
-    wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${genome_gencode_version}.tar.gz.ac
-    wget $args http://sourceforge.net/projects/fusioncatcher/files/data/human_${genome_gencode_version}.tar.gz.ad
-    cat human_${genome_gencode_version}.tar.gz.* | tar xz
-    rm human_${genome_gencode_version}.tar*
+    wget --no-check-certificate $args ${params.fusioncatcher_download_link}/human_v${genome_gencode_version}.tar.gz.partaa
+    wget --no-check-certificate $args ${params.fusioncatcher_download_link}/human_v${genome_gencode_version}.tar.gz.partab
+    wget --no-check-certificate $args ${params.fusioncatcher_download_link}/human_v${genome_gencode_version}.tar.gz.partac
+    cat human_v${genome_gencode_version}.tar.gz.* | tar xz
+    rm human_v${genome_gencode_version}.tar*
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+        wget: \$(wget --version | head -1 | cut -d ' ' -f 3)
+        tar: \$(tar --version | head -1 | sed -e 's/tar (GNU tar) //')
     END_VERSIONS
     """
 
@@ -41,7 +41,8 @@ process FUSIONCATCHER_DOWNLOAD {
     touch human_v${genome_gencode_version}/ensembl_fully_overlapping_genes.txt
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+        wget: \$(wget --version | head -1 | cut -d ' ' -f 3)
+        tar: \$(tar --version | head -1 | sed -e 's/tar (GNU tar) //')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/environment.yml b/modules/nf-core/fusioncatcher/fusioncatcher/environment.yml
new file mode 100644
index 000000000..25f7417c5
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::fusioncatcher=1.33"
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/main.nf b/modules/nf-core/fusioncatcher/fusioncatcher/main.nf
new file mode 100644
index 000000000..5c2a8f38d
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/main.nf
@@ -0,0 +1,65 @@
+process FUSIONCATCHER_FUSIONCATCHER {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fusioncatcher:1.33--hdfd78af_5':
+        'biocontainers/fusioncatcher:1.33--hdfd78af_5' }"
+
+    input:
+    tuple val(meta), path(fastqs)
+    tuple val(meta2), path(reference)
+
+    output:
+    tuple val(meta), path("*.fusion-genes.txt"), emit: fusions, optional: true
+    tuple val(meta), path("*.summary.txt")     , emit: summary, optional: true
+    tuple val(meta), path("*.log")             , emit: log
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input = fastqs.join(",")
+
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[FusionCatcher] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    fusioncatcher \\
+        --input=${input} \\
+        --output=. \\
+        --data=${reference} \\
+        --threads=${task.cpus} \\
+        --Xmx=${avail_mem} \\
+        ${args}
+
+    mv final-list_candidate-fusion-genes.txt ${prefix}.fusion-genes.txt
+    mv summary_candidate_fusions.txt ${prefix}.summary.txt
+    mv fusioncatcher.log ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fusion-genes.txt
+    touch ${prefix}.summary.txt
+    touch ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/meta.yml b/modules/nf-core/fusioncatcher/fusioncatcher/meta.yml
new file mode 100644
index 000000000..ff6647d65
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/meta.yml
@@ -0,0 +1,78 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "fusioncatcher_fusioncatcher"
+description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
+keywords:
+  - fusion
+  - rna
+  - fastq
+tools:
+  - fusioncatcher:
+      description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
+      homepage: https://github.com/ndaniel/fusioncatcher
+      documentation: https://github.com/ndaniel/fusioncatcher/wiki
+      tool_dev_url: https://github.com/ndaniel/fusioncatcher
+      doi: "10.1101/011650v1"
+      licence: ["GPL v3"]
+      identifier: biotools:fusioncatcher
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fastqs:
+        type: list
+        description: A list of input fastq files
+        pattern: "*.{fastq,fq}.gz"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reference:
+        type: file
+        description: Directory containing fusioncatcher reference files
+
+output:
+  - fusions:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.fusion-genes.txt":
+          type: file
+          description: The detected fusions in the input files
+          pattern: "*.fusion-genes.txt"
+  - summary:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.summary.txt":
+          type: file
+          description: The generated summary
+          pattern: "*.summary.txt"
+  - log:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.log":
+          type: file
+          description: The Fusioncatcher log
+          pattern: "*.log"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test b/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test
new file mode 100644
index 000000000..28e9d13ec
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test
@@ -0,0 +1,43 @@
+nextflow_process {
+
+    name "Test Process FUSIONCATCHER_FUSIONCATCHER"
+    script "../main.nf"
+    process "FUSIONCATCHER_FUSIONCATCHER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fusioncatcher"
+    tag "fusioncatcher/fusioncatcher"
+
+    // Only stub tests because the refernce is about 50 GB of data
+
+    test("sarscov2 - fastq - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'reference'],
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test.snap b/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test.snap
new file mode 100644
index 000000000..a1916e553
--- /dev/null
+++ b/modules/nf-core/fusioncatcher/fusioncatcher/tests/main.nf.test.snap
@@ -0,0 +1,73 @@
+{
+    "sarscov2 - fastq - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fusion-genes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,6a54daab2ec7621d8493678e832cf45e"
+                ],
+                "fusions": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fusion-genes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6a54daab2ec7621d8493678e832cf45e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T11:01:13.392512529"
+    }
+}
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index bbf508168..fa731713b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -60,7 +60,8 @@ params {
     skip_vcf                   = false
 
     // Download references option
-    download_refs              = false
+    download_refs               = false
+    fusioncatcher_download_link = "https://master.dl.sourceforge.net/project/rnafusion/fusioncatcher"
 
     // Path to references
     fasta                         = "${params.genomes_base}/gencode/Homo_sapiens_${params.genome}_${params.genome_gencode_version}_dna_primary_assembly.fa"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 42a158f9c..190b98292 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -156,6 +156,13 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to fusioncatcher references"
                 },
+                "fusioncatcher_download_link": {
+                    "type": "string",
+                    "description": "Fusioncatcher download link",
+                    "fa_icon": "far fa-file-code",
+                    "pattern": "^https?://.*$",
+                    "default": "https://master.dl.sourceforge.net/project/rnafusion/fusioncatcher"
+                },
                 "fusioninspector_limitSjdbInsertNsj": {
                     "type": "integer",
                     "fa_icon": "far fa-file-code",
diff --git a/subworkflows/local/build_references/main.nf b/subworkflows/local/build_references/main.nf
index 2a2bc1486..30a26db36 100644
--- a/subworkflows/local/build_references/main.nf
+++ b/subworkflows/local/build_references/main.nf
@@ -5,7 +5,7 @@
 */
 
 include { GENCODE_DOWNLOAD }                from '../../../modules/local/gencode_download/main'
-include { FUSIONCATCHER_BUILD }             from '../../../modules/local/fusioncatcher/build/main'
+include { FUSIONCATCHER_DOWNLOAD }          from '../../../modules/local/fusioncatcher/download/main'
 include { FUSIONREPORT_DOWNLOAD }           from '../../../modules/local/fusionreport/download/main'
 include { HGNC_DOWNLOAD }                   from '../../../modules/local/hgnc/main'
 include { STARFUSION_BUILD }                from '../../../modules/local/starfusion/build/main'
@@ -18,6 +18,7 @@ include { CTATSPLICING_PREPGENOMELIB }      from '../../../modules/local/ctatspl
     IMPORT NF-CORE MODULES/SUBWORKFLOWS
 ========================================================================================
 */
+
 include { ARRIBA_DOWNLOAD }                 from '../../../modules/nf-core/arriba/download/main'
 include { SAMTOOLS_FAIDX }                  from '../../../modules/nf-core/samtools/faidx/main'
 include { STAR_GENOMEGENERATE }             from '../../../modules/nf-core/star/genomegenerate/main'
@@ -155,9 +156,9 @@ workflow BUILD_REFERENCES {
     def ch_fusioncatcher_ref = Channel.empty()
     if (tools.contains("fusioncatcher")) {
         if (!exists_not_empty(params.fusioncatcher_ref)) {
-                FUSIONCATCHER_BUILD(params.genome_gencode_version)
-                ch_versions = ch_versions.mix(FUSIONCATCHER_BUILD.out.versions)
-                ch_fusioncatcher_ref = FUSIONCATCHER_BUILD.out.reference
+            FUSIONCATCHER_DOWNLOAD(params.genome_gencode_version)
+            ch_versions = ch_versions.mix(FUSIONCATCHER_DOWNLOAD.out.versions)
+            ch_fusioncatcher_ref = FUSIONCATCHER_DOWNLOAD.out.reference
         }
         else {
             ch_fusioncatcher_ref = Channel.fromPath(params.fusioncatcher_ref).map { it -> [[id:it.name], it] }
diff --git a/subworkflows/local/fusioncatcher_workflow/main.nf b/subworkflows/local/fusioncatcher_workflow/main.nf
index f500bc333..f4f053d2f 100644
--- a/subworkflows/local/fusioncatcher_workflow/main.nf
+++ b/subworkflows/local/fusioncatcher_workflow/main.nf
@@ -1,9 +1,8 @@
-include { FUSIONCATCHER_DETECT } from '../../../modules/local/fusioncatcher/detect/main'
+include { FUSIONCATCHER_FUSIONCATCHER } from '../../../modules/nf-core/fusioncatcher/fusioncatcher/main'
 
 // TODO: Remove fusioncatcher_fusions as parameter.
 // TODO: remove dummy file. Work with Channel.empty()
 // TODO: if the files were already produced and the user want to skip the module because of this, they should be taken them from the sample sheet
-// TODO: harmonize `fusioncatcher` and `fusioncatcher_only` parameters at main workflow level to activate/skip this one.
 
 workflow FUSIONCATCHER_WORKFLOW {
     take:
@@ -20,12 +19,12 @@ workflow FUSIONCATCHER_WORKFLOW {
                                         .map { meta, _reads, fusions -> [ meta, fusions ] }
         } else {
 
-            FUSIONCATCHER_DETECT (
+            FUSIONCATCHER_FUSIONCATCHER (
                 reads,
                 fusioncatcher_ref
             )
-            ch_fusioncatcher_fusions = FUSIONCATCHER_DETECT.out.fusions
-            ch_versions              = ch_versions.mix(FUSIONCATCHER_DETECT.out.versions)
+            ch_fusioncatcher_fusions = FUSIONCATCHER_FUSIONCATCHER.out.fusions
+            ch_versions              = ch_versions.mix(FUSIONCATCHER_FUSIONCATCHER.out.versions)
         }
 
     emit:
diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap
index 86f939825..d58e52dae 100644
--- a/tests/test_stub.nf.test.snap
+++ b/tests/test_stub.nf.test.snap
@@ -1199,10 +1199,11 @@
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
-                "FUSIONCATCHER_BUILD": {
-                    "fusioncatcher": "1.33"
+                "FUSIONCATCHER_DOWNLOAD": {
+                    "wget": "1.21.4",
+                    "tar": 1.35
                 },
-                "FUSIONCATCHER_DETECT": {
+                "FUSIONCATCHER_FUSIONCATCHER": {
                     "fusioncatcher": "1.33"
                 },
                 "FUSIONREPORT": {
@@ -1270,11 +1271,9 @@
                 "fastqc/test.html",
                 "fastqc/test.zip",
                 "fusioncatcher",
-                "fusioncatcher/human_v46",
-                "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
-                "fusioncatcher/test.fusioncatcher.fusion-genes.txt",
-                "fusioncatcher/test.fusioncatcher.log",
-                "fusioncatcher/test.fusioncatcher.summary.txt",
+                "fusioncatcher/test.fusion-genes.txt",
+                "fusioncatcher/test.log",
+                "fusioncatcher/test.summary.txt",
                 "fusionreport",
                 "fusionreport/test",
                 "fusionreport/test/AAA_BBB.html",
@@ -1315,6 +1314,9 @@
                 "references/fusion_report_db/fusion_report.log",
                 "references/fusion_report_db/fusiongdb2.db",
                 "references/fusion_report_db/mitelman.db",
+                "references/fusioncatcher",
+                "references/fusioncatcher/human_v46",
+                "references/fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
                 "references/gencode",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list",
@@ -1443,7 +1445,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-04-03T15:43:02.916057311"
+        "timestamp": "2025-04-16T10:39:10.08713305"
     },
     "stub test fastp": {
         "content": [
@@ -1526,10 +1528,11 @@
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
-                "FUSIONCATCHER_BUILD": {
-                    "fusioncatcher": "1.33"
+                "FUSIONCATCHER_DOWNLOAD": {
+                    "wget": "1.21.4",
+                    "tar": 1.35
                 },
-                "FUSIONCATCHER_DETECT": {
+                "FUSIONCATCHER_FUSIONCATCHER": {
                     "fusioncatcher": "1.33"
                 },
                 "GATK4_BEDTOINTERVALLIST": {
@@ -1559,11 +1562,9 @@
                 "fastqc/test.html",
                 "fastqc/test.zip",
                 "fusioncatcher",
-                "fusioncatcher/human_v46",
-                "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
-                "fusioncatcher/test.fusioncatcher.fusion-genes.txt",
-                "fusioncatcher/test.fusioncatcher.log",
-                "fusioncatcher/test.fusioncatcher.summary.txt",
+                "fusioncatcher/test.fusion-genes.txt",
+                "fusioncatcher/test.log",
+                "fusioncatcher/test.summary.txt",
                 "gatk4",
                 "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict",
                 "get",
@@ -1576,6 +1577,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml",
                 "references",
+                "references/fusioncatcher",
+                "references/fusioncatcher/human_v46",
+                "references/fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
                 "references/gencode",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list",
@@ -1588,7 +1592,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-04-03T15:40:58.774714515"
+        "timestamp": "2025-04-16T10:35:22.7562139"
     },
     "stub test all": {
         "content": [
@@ -1618,10 +1622,11 @@
                 "FASTQC_FOR_FASTP": {
                     "fastqc": "0.12.1"
                 },
-                "FUSIONCATCHER_BUILD": {
-                    "fusioncatcher": "1.33"
+                "FUSIONCATCHER_DOWNLOAD": {
+                    "wget": "1.21.4",
+                    "tar": 1.35
                 },
-                "FUSIONCATCHER_DETECT": {
+                "FUSIONCATCHER_FUSIONCATCHER": {
                     "fusioncatcher": "1.33"
                 },
                 "FUSIONINSPECTOR": {
@@ -1733,11 +1738,9 @@
                 "fastqc_for_fastp/test_trimmed.html",
                 "fastqc_for_fastp/test_trimmed.zip",
                 "fusioncatcher",
-                "fusioncatcher/human_v46",
-                "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
-                "fusioncatcher/test.fusioncatcher.fusion-genes.txt",
-                "fusioncatcher/test.fusioncatcher.log",
-                "fusioncatcher/test.fusioncatcher.summary.txt",
+                "fusioncatcher/test.fusion-genes.txt",
+                "fusioncatcher/test.log",
+                "fusioncatcher/test.summary.txt",
                 "fusioninspector",
                 "fusioninspector/IGV_inputs",
                 "fusioninspector/IGV_inputs/TrinityFusion.bed",
@@ -1897,6 +1900,9 @@
                 "references/fusion_report_db/fusion_report.log",
                 "references/fusion_report_db/fusiongdb2.db",
                 "references/fusion_report_db/mitelman.db",
+                "references/fusioncatcher",
+                "references/fusioncatcher/human_v46",
+                "references/fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
                 "references/gencode",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list",
@@ -2063,6 +2069,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-04-11T09:09:47.739799535"
+        "timestamp": "2025-04-16T10:32:08.583950433"
     }
 }
\ No newline at end of file
diff --git a/tests/test_stub_bam.nf.test.snap b/tests/test_stub_bam.nf.test.snap
index feb129fc2..ac8414578 100644
--- a/tests/test_stub_bam.nf.test.snap
+++ b/tests/test_stub_bam.nf.test.snap
@@ -1092,10 +1092,11 @@
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
-                "FUSIONCATCHER_BUILD": {
-                    "fusioncatcher": "1.33"
+                "FUSIONCATCHER_DOWNLOAD": {
+                    "wget": "1.21.4",
+                    "tar": 1.35
                 },
-                "FUSIONCATCHER_DETECT": {
+                "FUSIONCATCHER_FUSIONCATCHER": {
                     "fusioncatcher": "1.33"
                 },
                 "FUSIONREPORT": {
@@ -1155,11 +1156,9 @@
                 "fastqc/test.html",
                 "fastqc/test.zip",
                 "fusioncatcher",
-                "fusioncatcher/human_v46",
-                "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
-                "fusioncatcher/test.fusioncatcher.fusion-genes.txt",
-                "fusioncatcher/test.fusioncatcher.log",
-                "fusioncatcher/test.fusioncatcher.summary.txt",
+                "fusioncatcher/test.fusion-genes.txt",
+                "fusioncatcher/test.log",
+                "fusioncatcher/test.summary.txt",
                 "fusionreport",
                 "fusionreport/test",
                 "fusionreport/test/AAA_BBB.html",
@@ -1200,6 +1199,9 @@
                 "references/fusion_report_db/fusion_report.log",
                 "references/fusion_report_db/fusiongdb2.db",
                 "references/fusion_report_db/mitelman.db",
+                "references/fusioncatcher",
+                "references/fusioncatcher/human_v46",
+                "references/fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
                 "references/gencode",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list",
@@ -1309,7 +1311,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-04-10T10:11:07.156105951"
+        "timestamp": "2025-04-16T10:51:50.320939135"
     },
     "stub test fastp": {
         "content": [
@@ -1411,10 +1413,11 @@
                 "FASTQC": {
                     "fastqc": "0.12.1"
                 },
-                "FUSIONCATCHER_BUILD": {
-                    "fusioncatcher": "1.33"
+                "FUSIONCATCHER_DOWNLOAD": {
+                    "wget": "1.21.4",
+                    "tar": 1.35
                 },
-                "FUSIONCATCHER_DETECT": {
+                "FUSIONCATCHER_FUSIONCATCHER": {
                     "fusioncatcher": "1.33"
                 },
                 "GATK4_BEDTOINTERVALLIST": {
@@ -1454,11 +1457,9 @@
                 "fastqc/test.html",
                 "fastqc/test.zip",
                 "fusioncatcher",
-                "fusioncatcher/human_v46",
-                "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
-                "fusioncatcher/test.fusioncatcher.fusion-genes.txt",
-                "fusioncatcher/test.fusioncatcher.log",
-                "fusioncatcher/test.fusioncatcher.summary.txt",
+                "fusioncatcher/test.fusion-genes.txt",
+                "fusioncatcher/test.log",
+                "fusioncatcher/test.summary.txt",
                 "gatk4",
                 "gatk4/Homo_sapiens.GRCh38.46_dna_primary_assembly.dict",
                 "get",
@@ -1480,6 +1481,9 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_rnafusion_software_mqc_versions.yml",
                 "references",
+                "references/fusioncatcher",
+                "references/fusioncatcher/human_v46",
+                "references/fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
                 "references/gencode",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list",
@@ -1492,7 +1496,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-04-10T10:09:12.170433159"
+        "timestamp": "2025-04-16T10:48:04.746178504"
     },
     "stub test all": {
         "content": [
@@ -1522,10 +1526,11 @@
                 "FASTQC_FOR_FASTP": {
                     "fastqc": "0.12.1"
                 },
-                "FUSIONCATCHER_BUILD": {
-                    "fusioncatcher": "1.33"
+                "FUSIONCATCHER_DOWNLOAD": {
+                    "wget": "1.21.4",
+                    "tar": 1.35
                 },
-                "FUSIONCATCHER_DETECT": {
+                "FUSIONCATCHER_FUSIONCATCHER": {
                     "fusioncatcher": "1.33"
                 },
                 "FUSIONINSPECTOR": {
@@ -1629,11 +1634,9 @@
                 "fastqc_for_fastp/test_trimmed.html",
                 "fastqc_for_fastp/test_trimmed.zip",
                 "fusioncatcher",
-                "fusioncatcher/human_v46",
-                "fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
-                "fusioncatcher/test.fusioncatcher.fusion-genes.txt",
-                "fusioncatcher/test.fusioncatcher.log",
-                "fusioncatcher/test.fusioncatcher.summary.txt",
+                "fusioncatcher/test.fusion-genes.txt",
+                "fusioncatcher/test.log",
+                "fusioncatcher/test.summary.txt",
                 "fusioninspector",
                 "fusioninspector/IGV_inputs",
                 "fusioninspector/IGV_inputs/TrinityFusion.bed",
@@ -1793,6 +1796,9 @@
                 "references/fusion_report_db/fusion_report.log",
                 "references/fusion_report_db/fusiongdb2.db",
                 "references/fusion_report_db/mitelman.db",
+                "references/fusioncatcher",
+                "references/fusioncatcher/human_v46",
+                "references/fusioncatcher/human_v46/ensembl_fully_overlapping_genes.txt",
                 "references/gencode",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf",
                 "references/gencode/Homo_sapiens.GRCh38.46.gtf.interval_list",
@@ -1943,6 +1949,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-04-11T09:18:32.616357228"
+        "timestamp": "2025-04-16T10:44:36.932311827"
     }
 }
\ No newline at end of file


Reviews:
user: login: atrigila
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-04-15T16:33:07Z
user: login: atrigila
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-04-15T18:40:22Z
user: login: nvnieuwk
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-04-16T07:59:01Z
user: login: nvnieuwk
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-04-16T07:59:32Z
user: login: nvnieuwk
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-04-16T08:05:31Z
user: login: atrigila
body: Thanks for the refactoring work and for aligning the code with nf-core standards. I’m not able to test the changes locally at the moment, but since the updates are primarily related to structure and migration rather than new implementations, and these can be tested via stubs, they look sensible to me. If your own local test results confirm everything runs as expected, this looks good to me.
state: APPROVED
author_association: CONTRIBUTOR
submitted_at: 2025-04-16T12:57:45Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:11:10Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:11:40Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:11:50Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:12:07Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:12:23Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:12:32Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:13:35Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:13:52Z
user: login: rannick
state: COMMENTED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:16:25Z
user: login: nvnieuwk
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-04-22T09:17:19Z
user: login: rannick
body: LGTM
state: APPROVED
author_association: COLLABORATOR
submitted_at: 2025-04-22T09:22:28Z

Review comments:
diff_hunk: @@ -156,6 +156,17 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to fusioncatcher references"
                 },
+                "fusioncatcher_build": {
+                    "type": "boolean",
+                    "description": "Build fusioncatcher references instead of downloading them. This is required for any references other than for human gencode v46 at the moment."
+                },
+                "fusioncatcher_download_link": {
+                    "type": "string",
+                    "description": "Fusioncatcher download link",
+                    "fa_icon": "far fa-file-code",
+                    "pattern": "^https?://.*$",
+                    "default": "https://master.dl.sourceforge.net/project/rnafusion/fusioncatcher"
+                },
path: nextflow_schema.json
user: login: atrigila
body: We should eventually have our own references hosted in nf-core. https://github.com/nf-core/rnafusion/issues/515
created_at: 2025-04-15T16:27:22Z
author_association: CONTRIBUTOR
diff_hunk: @@ -2,17 +2,17 @@ process FUSIONCATCHER_DOWNLOAD {
     tag "fusioncatcher_download"
     label 'process_medium'
 
-    conda "${projectDir}/environment.yml"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' :
-        'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }"
+        'https://depot.galaxyproject.org/singularity/fusioncatcher:1.33--hdfd78af_5':
+        'biocontainers/fusioncatcher:1.33--hdfd78af_5' }"
path: modules/local/fusioncatcher/download/main.nf
user: login: atrigila
body: Any reason behind this change? Since it is all wget, perhaps we shouldn't even have this, right? 
created_at: 2025-04-15T18:40:22Z
author_association: CONTRIBUTOR
diff_hunk: @@ -156,6 +156,17 @@
                     "fa_icon": "far fa-file-code",
                     "description": "Path to fusioncatcher references"
                 },
+                "fusioncatcher_build": {
+                    "type": "boolean",
+                    "description": "Build fusioncatcher references instead of downloading them. This is required for any references other than for human gencode v46 at the moment."
+                },
+                "fusioncatcher_download_link": {
+                    "type": "string",
+                    "description": "Fusioncatcher download link",
+                    "fa_icon": "far fa-file-code",
+                    "pattern": "^https?://.*$",
+                    "default": "https://master.dl.sourceforge.net/project/rnafusion/fusioncatcher"
+                },
path: nextflow_schema.json
user: login: nvnieuwk
body: Yep that's the end goal!! Let's hope soon
created_at: 2025-04-16T07:59:01Z
author_association: CONTRIBUTOR
diff_hunk: @@ -2,17 +2,17 @@ process FUSIONCATCHER_DOWNLOAD {
     tag "fusioncatcher_download"
     label 'process_medium'
 
-    conda "${projectDir}/environment.yml"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' :
-        'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }"
+        'https://depot.galaxyproject.org/singularity/fusioncatcher:1.33--hdfd78af_5':
+        'biocontainers/fusioncatcher:1.33--hdfd78af_5' }"
path: modules/local/fusioncatcher/download/main.nf
user: login: nvnieuwk
body: The old container didn't have `wget`, but yes you are right it doesn't need the whole dependency of fusioncatcher
created_at: 2025-04-16T07:59:31Z
author_association: CONTRIBUTOR
diff_hunk: @@ -2,17 +2,17 @@ process FUSIONCATCHER_DOWNLOAD {
     tag "fusioncatcher_download"
     label 'process_medium'
 
-    conda "${projectDir}/environment.yml"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d5/d53f36e9e01d14a0ae8e15f8046f52b2883c970c27fe43fdfbd9440a55f5403f/data' :
-        'community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f' }"
+        'https://depot.galaxyproject.org/singularity/fusioncatcher:1.33--hdfd78af_5':
+        'biocontainers/fusioncatcher:1.33--hdfd78af_5' }"
path: modules/local/fusioncatcher/download/main.nf
user: login: nvnieuwk
body: I updated it, now it only uses wget 
created_at: 2025-04-16T08:05:31Z
author_association: CONTRIBUTOR
diff_hunk: @@ -85,6 +86,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed missing script `gtf2bed` which caused local module `GET_RRNA_TRANSCRIPTS` to fail [#602](https://github.com/nf-core/rnafusion/issues/602)
 - Fixed the codebase to be compatible with the Nextflow language server [#634](https://github.com/nf-core/rnafusion/pull/634)
 - Updated the input validation to be more strict. This will prevent more errors down the line in the pipeline [#640](https://github.com/nf-core/rnafusion/pull/640)
+- Fusioncatcher build should now work again [#650](https://github.com/nf-core/rnafusion/pull/650)
path: CHANGELOG.md
user: login: rannick
body: Needs an update
created_at: 2025-04-22T09:11:10Z
author_association: COLLABORATOR
diff_hunk: @@ -96,10 +98,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter        | New parameter       |
-| -------------------- | ------------------- |
-|                      | `--no_cosmic`       |
-| `--build_references` | `--references_only` |
+| Old parameter         | New parameter                   |
+| --------------------- | ------------------------------- |
+|                       | `--no_cosmic`                   |
+| `--build_references`  | `--references_only`             |
+| `--fastp_trim`        | `--tools`                       |
path: CHANGELOG.md
user: login: rannick
body: ```suggestion
| `--fastp_trim`        | `--tools fastp`                       |
```
created_at: 2025-04-22T09:11:40Z
author_association: COLLABORATOR
diff_hunk: @@ -96,10 +98,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter        | New parameter       |
-| -------------------- | ------------------- |
-|                      | `--no_cosmic`       |
-| `--build_references` | `--references_only` |
+| Old parameter         | New parameter                   |
+| --------------------- | ------------------------------- |
+|                       | `--no_cosmic`                   |
+| `--build_references`  | `--references_only`             |
+| `--fastp_trim`        | `--tools`                       |
+| `--arriba`            | `--tools`                       |
path: CHANGELOG.md
user: login: rannick
body: ```suggestion
| `--arriba`            | `--tools arriba`                       |
```
created_at: 2025-04-22T09:11:50Z
author_association: COLLABORATOR
diff_hunk: @@ -96,10 +98,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter        | New parameter       |
-| -------------------- | ------------------- |
-|                      | `--no_cosmic`       |
-| `--build_references` | `--references_only` |
+| Old parameter         | New parameter                   |
+| --------------------- | ------------------------------- |
+|                       | `--no_cosmic`                   |
+| `--build_references`  | `--references_only`             |
+| `--fastp_trim`        | `--tools`                       |
+| `--arriba`            | `--tools`                       |
+| `--ctatsplicing`      | `--tools`                       |
+| `--run_fusioncatcher` | `--tools`                       |
+| `--starfusion`        | `--tools`                       |
+| `--stringtie`         | `--tools`                       |
+| `--all`               | `--tools`                       |
+|                       | `--fusioncatcher_build`         |
path: CHANGELOG.md
user: login: rannick
body: ```suggestion
```
created_at: 2025-04-22T09:12:07Z
author_association: COLLABORATOR
diff_hunk: @@ -96,10 +98,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter        | New parameter       |
-| -------------------- | ------------------- |
-|                      | `--no_cosmic`       |
-| `--build_references` | `--references_only` |
+| Old parameter         | New parameter                   |
+| --------------------- | ------------------------------- |
+|                       | `--no_cosmic`                   |
+| `--build_references`  | `--references_only`             |
+| `--fastp_trim`        | `--tools`                       |
+| `--arriba`            | `--tools`                       |
+| `--ctatsplicing`      | `--tools`                       |
path: CHANGELOG.md
user: login: rannick
body: ```suggestion
| `--ctatsplicing`      | `--tools ctatsplicing`                       |
```
created_at: 2025-04-22T09:12:23Z
author_association: COLLABORATOR
diff_hunk: @@ -96,10 +98,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter        | New parameter       |
-| -------------------- | ------------------- |
-|                      | `--no_cosmic`       |
-| `--build_references` | `--references_only` |
+| Old parameter         | New parameter                   |
+| --------------------- | ------------------------------- |
+|                       | `--no_cosmic`                   |
+| `--build_references`  | `--references_only`             |
+| `--fastp_trim`        | `--tools`                       |
+| `--arriba`            | `--tools`                       |
+| `--ctatsplicing`      | `--tools`                       |
+| `--run_fusioncatcher` | `--tools`                       |
path: CHANGELOG.md
user: login: rannick
body: same as above
created_at: 2025-04-22T09:12:32Z
author_association: COLLABORATOR
diff_hunk: @@ -87,8 +87,20 @@ process {
         ]
     }
 
-    withName: 'FUSIONCATCHER' {
-        ext.args = "--limitSjdbInsertNsj ${params.fusioncatcher_limitSjdbInsertNsj}"
+    withName: 'FUSIONCATCHER_FUSIONCATCHER' {
+        ext.args = {[
+            "--limitSjdbInsertNsj ${params.fusioncatcher_limitSjdbInsertNsj}",
+            "--skip-blat",
+            meta.single_end ? "--single-end" : "",
+        ].join(' ')}
+    }
+
+    withName: 'FUSIONCATCHER_BUILD' {
+        publishDir = [
+            path: { "${params.genomes_base}/fusioncatcher" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
path: conf/modules.config
user: login: rannick
body: ```suggestion
```
created_at: 2025-04-22T09:13:35Z
author_association: COLLABORATOR
diff_hunk: @@ -40,6 +40,16 @@
                         "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
+                    "fusioncatcher/build": {
+                        "branch": "master",
+                        "git_sha": "5781b9eaa352f23756c3cc98525ee549bbcc612b",
+                        "installed_by": ["modules"]
+                    },
path: modules.json
user: login: rannick
body: ```suggestion
```
created_at: 2025-04-22T09:13:52Z
author_association: COLLABORATOR
diff_hunk: @@ -18,6 +18,8 @@ include { CTATSPLICING_PREPGENOMELIB }      from '../../../modules/local/ctatspl
     IMPORT NF-CORE MODULES/SUBWORKFLOWS
 ========================================================================================
 */
+
+include { FUSIONCATCHER_BUILD }             from '../../../modules/nf-core/fusioncatcher/build/main'
path: subworkflows/local/build_references/main.nf
user: login: rannick
body: should be download
created_at: 2025-04-22T09:16:25Z
author_association: COLLABORATOR
diff_hunk: @@ -18,6 +18,8 @@ include { CTATSPLICING_PREPGENOMELIB }      from '../../../modules/local/ctatspl
     IMPORT NF-CORE MODULES/SUBWORKFLOWS
 ========================================================================================
 */
+
+include { FUSIONCATCHER_BUILD }             from '../../../modules/nf-core/fusioncatcher/build/main'
path: subworkflows/local/build_references/main.nf
user: login: nvnieuwk
body: The download include is at the top of the local modules
created_at: 2025-04-22T09:17:18Z
author_association: CONTRIBUTOR

PR comments:
user: login: github-actions[bot]
created_at: 2025-04-11T09:57:18Z
body: ## `nf-core pipelines lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 31c9371

```diff
+| ✅ 221 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!
```

<details>

### :heavy_exclamation_mark: Test warnings:

* [pipeline_todos](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/pipeline_todos) - TODO string in `nextflow.config`: _Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0_
* [pipeline_todos](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/pipeline_todos) - TODO string in `ro-crate-metadata.json`: _"description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnafusion_logo_dark.png\">\n    <img alt=\"nf-core/rnafusion\" src=\"docs/images/nf-core-rnafusion_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnafusion)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnafusion-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnafusion)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnafusion** is a bioinformatics pipeline that ...\n\n TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\n```bash\nnextflow run nf-core/rnafusion \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnafusion/usage) and the [parameter documentation](https://nf-co.re/rnafusion/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnafusion/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnafusion/output).\n\n## Credits\n\nnf-core/rnafusion was originally written by Martin Proks, Annick Renevey.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnafusion` channel](https://nfcore.slack.com/channels/rnafusion) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/rnafusion for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",_
* [schema_lint](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/schema_lint) - Input mimetype is missing or empty
* [local_component_structure](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/local_component_structure) - fusioninspector_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

### :grey_question: Tests ignored:

* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `.github/CONTRIBUTING.md`
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `.github/PULL_REQUEST_TEMPLATE.md`

### :white_check_mark: Tests passed:

* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.gitattributes`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.gitignore`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.nf-core.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.editorconfig`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.prettierignore`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.prettierrc.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `CHANGELOG.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `CITATIONS.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `CODE_OF_CONDUCT.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `nextflow_schema.json`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `nextflow.config`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `README.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/.dockstore.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/CONTRIBUTING.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/config.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/PULL_REQUEST_TEMPLATE.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/workflows/branch.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/workflows/ci.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting_comment.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `assets/email_template.html`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `assets/email_template.txt`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `assets/sendmail_template.txt`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `assets/nf-core-rnafusion_logo_light.png`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `conf/modules.config`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `conf/test.config`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `conf/test_full.config`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-rnafusion_logo_light.png`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-rnafusion_logo_dark.png`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `docs/output.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `docs/README.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `docs/README.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `docs/usage.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `main.nf`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `assets/multiqc_config.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `conf/base.config`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `conf/igenomes.config`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `conf/igenomes_ignored.config`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awstest.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awsfulltest.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `modules.json`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File found: `ro-crate-metadata.json`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `.github/workflows/push_dockerhub.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `.markdownlint.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `.nf-core.yaml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `.yamllint.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `bin/markdown_to_html.r`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `conf/aws.config`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `docs/images/nf-core-rnafusion_logo.png`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `lib/Checks.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `lib/Completion.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `lib/NfcoreTemplate.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `lib/Utils.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `lib/Workflow.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowMain.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowRnafusion.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `parameters.settings.json`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `pipeline_template.yml`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `Singularity`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `lib/nfcore_external_java_deps.jar`
* [files_exist](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_exist) - File not found check: `.travis.yml`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Found nf-schema plugin
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.name`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.nextflowVersion`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.description`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.version`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.homePage`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `report.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `process.cpus`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `process.memory`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `process.time`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `params.outdir`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `params.input`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.mainScript`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `report.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.beforeText`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.afterText`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.command`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.summary.beforeText`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.summary.afterText`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.nf_required_version`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.container`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.singleEnd`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.igenomesIgnore`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.name`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.enable_conda`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_cpus`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_memory`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_time`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationFailUnrecognisedParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationLenientMode`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationSchemaIgnoreParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationShowHiddenParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config ``timeline.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config ``report.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config ``trace.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config ``dag.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config ``manifest.name`` began with ``nf-core/``
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config ``dag.file`` ended with ``.html``
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.nextflowVersion`` started with >= or !>=
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config ``manifest.version`` ends in ``dev``: ``4.0.0dev``
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_version` is set to `master`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Lines for loading custom profiles found
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - nextflow.config contains configuration profile `test`
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.read_length= 100
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.fusioncatcher_limitSjdbInsertNsj= 2000000
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.fusioncatcher_download_link= https://master.dl.sourceforge.net/project/rnafusion/fusioncatcher
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.fusioninspector_limitSjdbInsertNsj= 1000000
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ctatsplicing_cancer_introns= https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/CANCER_SPLICING_LIB_SUPPLEMENT/cancer_introns.GRCh38.Jun232020.tsv.gz
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.tools_cutoff= 1
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.species= homo_sapiens
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dfam_version= 3.4
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_version= master
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.publish_dir_mode= copy
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_multiqc_email_size= 25.MB
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.validate_params= true
* [nextflow_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nextflow_config) - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.gitattributes` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.prettierrc.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `CODE_OF_CONDUCT.md` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `LICENSE` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.github/.dockstore.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/config.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.github/workflows/branch.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting_comment.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `assets/email_template.html` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `assets/email_template.txt` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `assets/sendmail_template.txt` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `assets/nf-core-rnafusion_logo_light.png` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-rnafusion_logo_light.png` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-rnafusion_logo_dark.png` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `docs/README.md` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.gitignore` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/files_unchanged) - `.prettierignore` matches the template
* [actions_ci](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' is triggered on expected events
* [actions_ci](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' checks minimum NF version
* [actions_awstest](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_awstest) - '.github/workflows/awstest.yml' is triggered correctly
* [actions_awsfulltest](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` is triggered correctly
* [actions_awsfulltest](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` does not use `-profile test`
* [readme](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/readme) - README Nextflow minimum version badge matched config. Badge: `24.04.2`, Config: `24.04.2`
* [readme](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/readme) - README Zenodo placeholder was replaced with DOI.
* [plugin_includes](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/plugin_includes) - No wrong validation plugin imports have been found
* [pipeline_name_conventions](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/pipeline_name_conventions) - Name adheres to nf-core convention
* [template_strings](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/template_strings) - Did not find any Jinja template strings (0 files)
* [schema_lint](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/schema_lint) - Schema lint passed
* [schema_lint](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/schema_lint) - Schema title + description lint passed
* [schema_params](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/schema_params) - Schema matched params returned from nextflow config
* [system_exit](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/system_exit) - No `System.exit` calls found
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: download_pipeline.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: ci.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: release-announcements.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: branch.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting_comment.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: template_version_comment.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awstest.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awsfulltest.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: clean-up.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: fix-linting.yml
* [merge_markers](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/merge_markers) - No merge markers found in pipeline files
* [modules_json](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_json) - Only installed modules found in `modules.json`
* [multiqc_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` found and not ignored.
* [multiqc_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `report_section_order`
* [multiqc_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `export_plots`
* [multiqc_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `report_comment`
* [multiqc_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` follows the ordering scheme of the minimally required plugins.
* [multiqc_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains a matching 'report_comment'.
* [multiqc_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains 'export_plots: true'.
* [modules_structure](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_structure) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
* [local_component_structure](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/local_component_structure) - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
* [base_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/base_config) - `conf/base.config` found and not ignored.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `conf/modules.config` found and not ignored.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `ARRIBA_ARRIBA` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `ARRIBA_DOWNLOAD` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `ARRIBA_VISUALISATION` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `CTATSPLICING_STARTOCANCERINTRONS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `GENCODE_DOWNLOAD` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `FASTP` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `FASTQC` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `FASTQC_FOR_FASTP` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `FUSIONCATCHER_FUSIONCATCHER` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `FUSIONCATCHER_DOWNLOAD` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `FUSIONREPORT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `FUSIONREPORT_DOWNLOAD` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `GATK4_BEDTOINTERVALLIST` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `GATK4_MARKDUPLICATES` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `GFFREAD` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `GTF_TO_REFFLAT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `HGNC_DOWNLOAD` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `MULTIQC` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `PICARD_COLLECTINSERTSIZEMETRICS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `SALMON_INDEX` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `SALMON_QUANT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `SAMTOOLS_FAIDX` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `SAMTOOLS_CONVERT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `SAMTOOLS_INDEX` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `STAR_ALIGN` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `STAR_GENOMEGENERATE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `STARFUSION_BUILD` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `CTATSPLICING_PREPGENOMELIB` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/modules_config) - `STRINGTIE_MERGE` found in `conf/modules.config` and Nextflow scripts.
* [nfcore_yml](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nfcore_yml) - Repository type in `.nf-core.yml` is valid: `pipeline`
* [nfcore_yml](https://nf-co.re/tools/docs/3.2.0/pipeline_lint_tests/nfcore_yml) - nf-core version in `.nf-core.yml` is set to the latest version: `3.2.0`

### Run details

* nf-core/tools version 3.2.0
* Run at `2025-04-22 09:18:24`

</details>

<!-- Sticky Pull Request Comment -->
author_association: NONE
user: login: nvnieuwk
created_at: 2025-04-16T13:04:28Z
body: Hi yes I've managed to run `FUSIONCATCHER_DOWNLOAD` sucessfully, `FUSIONCATCHER_BUILD` failed but it was already failing for me before...
author_association: CONTRIBUTOR
user: login: rannick
created_at: 2025-04-16T13:41:51Z
body: We can delete fusioncatcher_build from the pipeline in favor of download only for this release
author_association: COLLABORATOR
user: login: nvnieuwk
created_at: 2025-04-17T07:00:51Z
body: > We can delete fusioncatcher_build from the pipeline in favor of download only for this release

Yes good idea, maybe we keep the build process in but have the download process as the default (which is now the case)? 
author_association: CONTRIBUTOR
user: login: rannick
created_at: 2025-04-17T12:25:46Z
body: We can let it in but remove calls to it, because it will definitely not work anymore
author_association: COLLABORATOR
user: login: nvnieuwk
created_at: 2025-04-17T12:58:30Z
body: Allright I'll remove the option
author_association: CONTRIBUTOR
user: login: nvnieuwk
created_at: 2025-04-22T09:09:01Z
body: @rannick is this PR okay for you?
author_association: CONTRIBUTOR
user: login: nvnieuwk
created_at: 2025-04-22T09:15:43Z
body: Review comments have been addressed :)
author_association: CONTRIBUTOR