diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 251f5034..71ff7245 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -5,11 +5,18 @@ on:
     branches:
       - dev
   pull_request:
+    branches:
+      - dev
+      - master
   release:
     types: [published]
   workflow_dispatch:
 
 env:
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
@@ -20,35 +27,36 @@ concurrency:
 
 jobs:
   test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
+    name: "${{ matrix.NXF_VER }} | ${{ matrix.test_profile }} | ${{ matrix.compute_profile }}"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnafusion') }}"
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER:
           - "24.04.2"
           - "latest-stable"
-        trim_parameters:
-          - "--fastp_trim false"
-          - "--fastp_trim true"
-        profile:
-          - "conda"
+        test_profile:
+          - "test_stub"
+          - "test_build"
+        compute_profile:
           - "docker"
           - "singularity"
-        test_name:
-          - "test"
+          - "conda"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
         exclude:
           - isMaster: false
-            profile: "conda"
+            compute_profile: "conda"
           - isMaster: false
-            profile: "singularity"
+            compute_profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -56,17 +64,17 @@ jobs:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Set up Apptainer
-        if: matrix.profile == 'singularity'
+        if: matrix.compute_profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
 
       - name: Set up Singularity
-        if: matrix.profile == 'singularity'
+        if: matrix.compute_profile == 'singularity'
         run: |
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
       - name: Set up Miniconda
-        if: matrix.profile == 'conda'
+        if: matrix.compute_profile == 'conda'
         uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
         with:
           miniconda-version: "latest"
@@ -75,7 +83,7 @@ jobs:
           channels: conda-forge,bioconda
 
       - name: Set up Conda
-        if: matrix.profile == 'conda'
+        if: matrix.compute_profile == 'conda'
         run: |
           echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
           echo $(realpath python) >> $GITHUB_PATH
@@ -83,16 +91,32 @@ jobs:
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: "Run pipeline build with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} \
-          -stub --build_references \
-          --outdir /home/runner/work/rnafusion/rnafusion/results --all \
-          --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \
-          --no_cosmic
+          python -m pip install --upgrade pip
+          pip install pdiff
+
+      - uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
 
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+      - name: Run Tests (${{matrix.NXF_VER}} | ${{matrix.test_profile}} | ${{matrix.compute_profile}})
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} -stub \
-          --outdir /home/runner/work/rnafusion/rnafusion/results --all ${{ matrix.trim_parameters }} \
-          --genomes_base /home/runner/work/rnafusion/rnafusion/results/references
+          nf-test test \
+              --ci \
+              --tag ${{matrix.test_profile}} \
+              --profile "+${{ matrix.compute_profile }}" \
+              --junitxml=test.xml \
+              --debug --verbose
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
+          annotate_only: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a1a68d62..dc343325 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local module: `ENSEMBL_DOWNLOAD` [#539](https://github.com/nf-core/rnafusion/pull/539)
 - Add nf-test to local module: `HGNC_DOWNLOAD` [#540](https://github.com/nf-core/rnafusion/pull/540)
 - Add nf-test to local subworkflow: `STRINGTIE_WORKFLOW` [#541](https://github.com/nf-core/rnafusion/pull/541)
-- Option to avoid using COSMIC (for example in the case of clinical use) [547](https://github.com/nf-core/rnafusion/pull/547)
+- Option to avoid using COSMIC (for example in the case of clinical use) [#547](https://github.com/nf-core/rnafusion/pull/547)
 - Add nf-test to nf-core module: `PICARD_COLLECTRNASEQMETRICS` and update module [#551](https://github.com/nf-core/rnafusion/pull/551)
 - Add `--skip_vcf` boolean parameter to skip vcf file generation [#554](https://github.com/nf-core/rnafusion/pull/554)
 - Add nf-test to local module: `FUSIONREPORT_DOWNLOAD` [#560](https://github.com/nf-core/rnafusion/pull/560)
diff --git a/conf/igenomes.config b/conf/igenomes.config
new file mode 100644
index 00000000..d608b45b
--- /dev/null
+++ b/conf/igenomes.config
@@ -0,0 +1,478 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for iGenomes paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines reference genomes using iGenome paths.
+    Can be used by any config that customises the base path using:
+        $params.igenomes_base / --igenomes_base
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    // illumina iGenomes reference file paths
+    genomes {
+        'GRCh37' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
+            mito_name   = "MT"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed"
+            mirtrace_species = "hsa"
+        }
+        'GRCh38' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
+            mirtrace_species = "hsa"
+        }
+        'CHM13' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
+            bwamem2     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf"
+            gff         = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz"
+            mito_name   = "chrM"
+        }
+        'GRCm38' {
+            fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
+            mito_name   = "MT"
+            macs_gsize  = "1.87e9"
+            blacklist   = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed"
+            mirtrace_species = "mmu"
+        }
+        'TAIR10' {
+            fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
+            mito_name   = "Mt"
+            mirtrace_species = "ath"
+        }
+        'EB2' {
+            fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
+            // mirtrace_species = "bsu"
+        }
+        'UMD3.1' {
+            fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
+            mito_name   = "MT"
+            mirtrace_species = "bta"
+        }
+        'WBcel235' {
+            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
+            mito_name   = "MtDNA"
+            macs_gsize  = "9e7"
+            mirtrace_species = "cel"
+        }
+        'CanFam3.1' {
+            fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
+            mito_name   = "MT"
+            mirtrace_species = "cfa"
+        }
+        'GRCz10' {
+            fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+            mirtrace_species = "dre"
+        }
+        'BDGP6' {
+            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
+            mito_name   = "M"
+            macs_gsize  = "1.2e8"
+            mirtrace_species = "dme"
+        }
+        'EquCab2' {
+            fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
+            mito_name   = "MT"
+            // mirtrace_species = "ecb"
+        }
+        'EB1' {
+            fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
+            // mirtrace_species = "ecd"
+        }
+        'Galgal4' {
+            fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+            mirtrace_species = "gga"
+        }
+        'Gm01' {
+            fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
+            // mirtrace_species = "gmx"
+        }
+        'Mmul_1' {
+            fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
+            mito_name   = "MT"
+            // mirtrace_species = "mcc"
+        }
+        'IRGSP-1.0' {
+            fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
+            mito_name   = "Mt"
+            mirtrace_species = "osa"
+        }
+        'CHIMP2.1.4' {
+            fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
+            mito_name   = "MT"
+            mirtrace_species = "ptr"
+        }
+        'Rnor_5.0' {
+            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+            mirtrace_species = "rno"
+        }
+        'Rnor_6.0' {
+            fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+            mirtrace_species = "rno"
+        }
+        'R64-1-1' {
+            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
+            mito_name   = "MT"
+            macs_gsize  = "1.2e7"
+            // mirtrace_species = "sce"
+        }
+        'EF2' {
+            fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
+            mito_name   = "MT"
+            macs_gsize  = "1.21e7"
+            // mirtrace_species = "spo"
+        }
+        'Sbi1' {
+            fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
+            mirtrace_species = "sbi"
+        }
+        'Sscrofa10.2' {
+            fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
+            mito_name   = "MT"
+            mirtrace_species = "ssc"
+        }
+        'AGPv3' {
+            fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
+            mito_name   = "Mt"
+            mirtrace_species = "zma"
+        }
+        'hg38' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/hg38-blacklist.bed"
+            mirtrace_species = "hsa"
+        }
+        'hg19' {
+            fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "2.7e9"
+            blacklist   = "${projectDir}/assets/blacklists/hg19-blacklist.bed"
+            mirtrace_species = "hsa"
+        }
+        'mm10' {
+            fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "1.87e9"
+            blacklist   = "${projectDir}/assets/blacklists/mm10-blacklist.bed"
+            mirtrace_species = "mmu"
+        }
+        'bosTau8' {
+            fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            mirtrace_species = "bta"
+        }
+        'ce10' {
+            fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "9e7"
+            mirtrace_species = "cel"
+        }
+        'canFam3' {
+            fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
+            mito_name   = "chrM"
+            mirtrace_species = "cfa"
+        }
+        'danRer10' {
+            fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "1.37e9"
+            mirtrace_species = "dre"
+        }
+        'dm6' {
+            fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            macs_gsize  = "1.2e8"
+            mirtrace_species = "dme"
+        }
+        'equCab2' {
+            fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
+            mito_name   = "chrM"
+            // mirtrace_species = "ecb"
+        }
+        'galGal4' {
+            fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
+            mito_name   = "chrM"
+            mirtrace_species = "gga"
+        }
+        'panTro4' {
+            fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
+            mito_name   = "chrM"
+            mirtrace_species = "ptr"
+        }
+        'rn6' {
+            fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
+            mito_name   = "chrM"
+            mirtrace_species = "rno"
+        }
+        'sacCer3' {
+            fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
+            readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
+            mito_name   = "chrM"
+            macs_gsize  = "1.2e7"
+            // mirtrace_species = "sce"
+        }
+        'susScr3' {
+            fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
+            bwa         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
+            bowtie2     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/"
+            star        = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/"
+            bismark     = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
+            gtf         = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
+            bed12       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
+            readme      = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
+            mito_name   = "chrM"
+            mirtrace_species = "ssc"
+        }
+    }
+}
diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config
new file mode 100644
index 00000000..b4034d82
--- /dev/null
+++ b/conf/igenomes_ignored.config
@@ -0,0 +1,9 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for iGenomes paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Empty genomes dictionary to use when igenomes is ignored.
+----------------------------------------------------------------------------------------
+*/
+
+params.genomes = [:]
diff --git a/conf/test.config b/conf/test.config
index aa51522d..3cafa252 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -10,14 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
diff --git a/conf/test_build.config b/conf/test_build.config
new file mode 100644
index 00000000..616d734f
--- /dev/null
+++ b/conf/test_build.config
@@ -0,0 +1,24 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/rnafusion -profile test_build,<docker/singularity> --outdir <OUTDIR> -stub
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test build references profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Input data
+    build_references           = true
+    input                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
+    no_cosmic                  = true
+    all                        = true
+
+    skip_salmon_index          = true
+}
diff --git a/conf/test_cosmic.config b/conf/test_cosmic.config
new file mode 100644
index 00000000..cf199da4
--- /dev/null
+++ b/conf/test_cosmic.config
@@ -0,0 +1,22 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/rnafusion -profile test_cosmic,<docker/singularity> --outdir <OUTDIR> -stub
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test cosmic profile'
+    config_profile_description = 'Minimal test cosmic dataset to check pipeline function'
+
+    // Input data
+    input                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
+    all                    = true
+    cosmic_username        = secrets.COSMIC_USERNAME
+    cosmic_passwd          = secrets.COSMIC_PASSWD
+}
diff --git a/conf/test_full.config b/conf/test_full.config
index eb8f5cd6..cfcb7865 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -14,7 +14,9 @@ params {
 
     // Input data for full size test
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
-
-    // Other params
+    all   = true
+    // TODO
+    // test_full can't run currently because the references must be given and they are not available.
+    // This profile should be updated once they get uploaded.
 
     }
diff --git a/modules/local/fusioninspector/environment.yml b/modules/local/fusioninspector/environment.yml
new file mode 100644
index 00000000..06a9828a
--- /dev/null
+++ b/modules/local/fusioninspector/environment.yml
@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::dfam=3.7
+  - bioconda::hmmer=3.4
+  - bioconda::star-fusion=1.7.0
+  - bioconda::trinity=2.15.2
+  - bioconda::samtools=1.21
+  - bioconda::star=2.7.11b
diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf
index 2f99c711..ae05ceb4 100644
--- a/modules/local/fusioninspector/main.nf
+++ b/modules/local/fusioninspector/main.nf
@@ -2,8 +2,8 @@ process FUSIONINSPECTOR {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::dfam=3.7 bioconda::hmmer=3.4 bioconda::star-fusion=1.13.0 bioconda::trinity=2.15.1 bioconda::samtools=1.19.2 bioconda::star=2.7.11b"
-    container 'docker.io/trinityctat/starfusion:1.13.0'
+    conda "${moduleDir}/environment.yml"
+    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
 
     input:
     tuple val(meta), path(reads), path(fusion_list)
diff --git a/modules/local/starfusion/build/environment.yml b/modules/local/starfusion/build/environment.yml
new file mode 100644
index 00000000..06a9828a
--- /dev/null
+++ b/modules/local/starfusion/build/environment.yml
@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::dfam=3.7
+  - bioconda::hmmer=3.4
+  - bioconda::star-fusion=1.7.0
+  - bioconda::trinity=2.15.2
+  - bioconda::samtools=1.21
+  - bioconda::star=2.7.11b
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index a768cc5c..6ac3c694 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -1,8 +1,8 @@
 process STARFUSION_BUILD {
     tag 'star-fusion'
 
-    conda "bioconda::dfam=3.7 bioconda::hmmer=3.4 bioconda::star-fusion=1.13.0 bioconda::trinity=2.15.1 bioconda::samtools=1.19.2 bioconda::star=2.7.11b"
-    container "docker.io/trinityctat/starfusion:1.13.0"
+    conda "${moduleDir}/environment.yml"
+    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/starfusion/detect/environment.yml b/modules/local/starfusion/detect/environment.yml
new file mode 100644
index 00000000..06a9828a
--- /dev/null
+++ b/modules/local/starfusion/detect/environment.yml
@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::dfam=3.7
+  - bioconda::hmmer=3.4
+  - bioconda::star-fusion=1.7.0
+  - bioconda::trinity=2.15.2
+  - bioconda::samtools=1.21
+  - bioconda::star=2.7.11b
diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
index 9a46cc00..27396770 100644
--- a/modules/local/starfusion/detect/main.nf
+++ b/modules/local/starfusion/detect/main.nf
@@ -2,8 +2,8 @@ process STARFUSION {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::dfam=3.7 bioconda::hmmer=3.4 bioconda::star-fusion=1.13.0 bioconda::trinity=2.15.1 bioconda::samtools=1.19.2 bioconda::star=2.7.11b"
-    container 'docker.io/trinityctat/starfusion:1.13.0'
+    conda "${moduleDir}/environment.yml"
+    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
 
     input:
     tuple val(meta), path(reads), path(junction)
diff --git a/modules/local/starfusion/download/environment.yml b/modules/local/starfusion/download/environment.yml
new file mode 100644
index 00000000..06a9828a
--- /dev/null
+++ b/modules/local/starfusion/download/environment.yml
@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::dfam=3.7
+  - bioconda::hmmer=3.4
+  - bioconda::star-fusion=1.7.0
+  - bioconda::trinity=2.15.2
+  - bioconda::samtools=1.21
+  - bioconda::star=2.7.11b
diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
index 221d12dd..d0668486 100644
--- a/modules/local/starfusion/download/main.nf
+++ b/modules/local/starfusion/download/main.nf
@@ -1,8 +1,8 @@
 process STARFUSION_DOWNLOAD {
     tag 'star-fusion'
 
-    conda "bioconda::dfam=3.7 bioconda::hmmer=3.4 bioconda::star-fusion=1.13.0 bioconda::trinity=2.15.1 bioconda::samtools=1.19.2 bioconda::star=2.7.11b"
-    container 'docker.io/trinityctat/starfusion:1.13.0'
+    conda "${moduleDir}/environment.yml"
+    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
 
     output:
     path "ctat_genome_lib_build_dir/*"            , emit: reference
diff --git a/nextflow.config b/nextflow.config
index 0517254c..d436182c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -72,6 +72,7 @@ params {
     skip_qc                    = false
     skip_vis                   = false
     skip_vcf                   = false
+    skip_salmon_index          = false
 
     // Path to references
     no_cosmic                     = false
@@ -224,7 +225,13 @@ profiles {
     test {
         includeConfig 'conf/test.config'
     }
-    test_full {
+    test_build {
+        includeConfig 'conf/test_build.config'
+    }
+    test_cosmic {
+        includeConfig 'conf/test_cosmic.config'
+    }
+        test_full {
         includeConfig 'conf/test_full.config'
     }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e5d3866d..017a19fb 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -22,6 +22,11 @@
                 "skip_vcf": {
                     "type": "boolean",
                     "description": "Skip vcf generation step"
+                },
+                "skip_salmon_index": {
+                    "type": "boolean",
+                    "description": "Skip salmon index generation step",
+                    "hidden": true
                 }
             },
             "fa_icon": "fas fa-fast-forward"
diff --git a/nf-test.config b/nf-test.config
index 870799df..3ee9cc13 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,8 +1,14 @@
 config {
-
+    // location for all nf-tests
     testsDir "tests"
+
+    // nf-test directory including temporary files for each test
     workDir ".nf-test"
+
+    // location of an optional nextflow.config file specific for executing tests
     configFile "tests/nextflow.config"
-    profile ""
 
+    plugins {
+        load "nft-utils@0.0.3"
+    }
 }
diff --git a/tests/.nftignore b/tests/.nftignore
new file mode 100644
index 00000000..54792ea8
--- /dev/null
+++ b/tests/.nftignore
@@ -0,0 +1,5 @@
+pipeline_info/*.{html,json,txt,yml}
+references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz
+references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
+references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa
+references/hgnc/HGNC-DB-timestamp.txt
diff --git a/tests/main.nf.test b/tests/main.nf.test
deleted file mode 100644
index 715335d8..00000000
--- a/tests/main.nf.test
+++ /dev/null
@@ -1,49 +0,0 @@
-nextflow_pipeline {
-
-    name "Test pipeline"
-    script "../main.nf"
-    tag "pipeline"
-    tag "pipeline_rnafusion"
-
-    test("Run build references with profile test") {
-
-        when {
-            params {
-                build_references             = true
-                outdir                       = "results"
-                genome_base                  = "references"
-                max_cpus                     = 2
-                max_memory                   = '6.GB'
-                max_time                     = '6.h'
-                input                        = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
-                cosmic_username              = COSMIC_USERNAME
-                cosmic_passwd                = COSMIC_PASSWD
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-    test("Run fusion detection with profile test") {
-
-        when {
-            params {
-                outdir                       = "results"
-                genome_base                  = "references"
-                max_cpus                     = 2
-                max_memory                   = '6.GB'
-                max_time                     = '6.h'
-                input                        = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv'
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success }
-            )
-        }
-    }
-}
diff --git a/tests/nextflow.config b/tests/nextflow.config
index ebd067ac..c3f050dc 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,35 +1,8 @@
-/*
-========================================================================================
-    Nextflow config file for running tests
-========================================================================================
-*/
-
-params {
-    // Base directory for nf-core/modules test data
-    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
-
-    // Base directory for nf-core/rnaseq test data
-    pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/'
-
-    outdir = 'results'
-}
-
-// Impose sensible resource limits for testing
+// Limit and standardize resources for github actions and reproducibility
 process {
-    withName: '.*' {
-        cpus   = 2
-        memory = 3.GB
-        time   = 2.h
-    }
-}
-
-// Impose same minimum Nextflow version as the pipeline for testing
-manifest {
-    nextflowVersion = '!>=23.04.0'
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
 }
-
-// Disable all Nextflow reporting options
-timeline { enabled = false }
-report   { enabled = false }
-trace    { enabled = false }
-dag      { enabled = false }
diff --git a/tests/test_build.nf.test b/tests/test_build.nf.test
new file mode 100644
index 00000000..1999a3b4
--- /dev/null
+++ b/tests/test_build.nf.test
@@ -0,0 +1,36 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    profile "test_build"
+    tag "pipeline"
+    tag "pipeline_rnafusion"
+    tag "test_build"
+
+    test("test_build") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                all    = false // Output files when running all are too big for CI
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/test_build.nf.test.snap b/tests/test_build.nf.test.snap
new file mode 100644
index 00000000..3b5441dc
--- /dev/null
+++ b/tests/test_build.nf.test.snap
@@ -0,0 +1,47 @@
+{
+    "test_build": {
+        "content": [
+            [
+                "bedops",
+                "bedops/Homo_sapiens.GRCh38.102_rrna_intervals.gtf.bed",
+                "gatk4",
+                "gatk4/Homo_sapiens.GRCh38.102.dna.primary_assembly.dict",
+                "gffread",
+                "gffread/Homo_sapiens.GRCh38.102.fasta",
+                "pipeline_info",
+                "references",
+                "references/ensembl",
+                "references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf",
+                "references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa",
+                "references/ensembl/Homo_sapiens.GRCh38.102.dna.primary_assembly.fa.fai",
+                "references/ensembl/Homo_sapiens.GRCh38.102.genepred",
+                "references/ensembl/Homo_sapiens.GRCh38.102.gtf",
+                "references/ensembl/Homo_sapiens.GRCh38.102.refflat",
+                "references/ensembl/Homo_sapiens.GRCh38.102_rrna_intervals.gtf.interval_list",
+                "references/hgnc",
+                "references/hgnc/HGNC-DB-timestamp.txt",
+                "references/hgnc/hgnc_complete_set.txt",
+                "rrnatranscripts",
+                "rrnatranscripts/Homo_sapiens.GRCh38.102_rrna_intervals.gtf"
+            ],
+            [
+                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf.bed:md5,5bc3ccc76735ae46699a75269f0ea65b",
+                "Homo_sapiens.GRCh38.102.dna.primary_assembly.dict:md5,092f1bf29fce906ff7b5ece02b4b21c8",
+                "Homo_sapiens.GRCh38.102.fasta:md5,d1f17b045dc60c49f2cc29e30006afc0",
+                "Homo_sapiens.GRCh38.102.chr.gtf:md5,0069687307852c63596b4d2ebdbbaf0c",
+                "Homo_sapiens.GRCh38.102.dna.primary_assembly.fa.fai:md5,d527f3eb6b664020cf4d882b5820056f",
+                "Homo_sapiens.GRCh38.102.genepred:md5,59c577ca4ab033c0ce1feac1e387bcab",
+                "Homo_sapiens.GRCh38.102.gtf:md5,defac755cd9aa4e82ec33398c27745ef",
+                "Homo_sapiens.GRCh38.102.refflat:md5,ef095e13743811c31d44752c32e9673e",
+                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf.interval_list:md5,0abf61877f65247b15c438d605d85599",
+                "hgnc_complete_set.txt:md5,34f4bd879d972e511fcb0318df9775b6",
+                "Homo_sapiens.GRCh38.102_rrna_intervals.gtf:md5,744bf505deb50837b15441e808cad345"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-04T17:55:45.068780109"
+    }
+}
\ No newline at end of file
diff --git a/tests/test_cosmic.nf.test b/tests/test_cosmic.nf.test
new file mode 100644
index 00000000..9a56e76e
--- /dev/null
+++ b/tests/test_cosmic.nf.test
@@ -0,0 +1,101 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    profile "test_cosmic"
+    tag "pipeline"
+    tag "pipeline_rnafusion"
+    tag "test_cosmic"
+
+    test("test cosmic with fastp trim") {
+
+        when {
+            params {
+                outdir               = "$outputDir"
+                fastp_trim           = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("test cosmic no fastp trim") {
+
+        when {
+            params {
+                outdir     = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("test cosmic no fastp trim build") {
+
+        when {
+            params {
+                outdir           = "$outputDir"
+                build_references = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/test_stub.nf.test b/tests/test_stub.nf.test
new file mode 100644
index 00000000..41c7194f
--- /dev/null
+++ b/tests/test_stub.nf.test
@@ -0,0 +1,71 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    profile "test"
+    options "-stub" // TODO remove once reference files are available
+    tag "pipeline"
+    tag "pipeline_rnafusion"
+    tag "test_stub"
+
+    test("stub test with fastp trim") {
+
+        when {
+            params {
+                outdir          = "$outputDir"
+                fastp_trim      = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            // def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') //TODO uncomment once -stub is removed
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    // stable_path // TODO uncomment once -stub is removed
+                ).match() }
+            )
+        }
+    }
+
+    test("stub test no fastp trim") {
+
+        when {
+            params {
+                outdir          = "$outputDir"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            // def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') //TODO uncomment once -stub is removed
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    // stable_path // TODO uncomment once -stub is removed
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/test_stub.nf.test.snap b/tests/test_stub.nf.test.snap
new file mode 100644
index 00000000..3b83c240
--- /dev/null
+++ b/tests/test_stub.nf.test.snap
@@ -0,0 +1,105 @@
+{
+    "stub test no fastp trim": {
+        "content": [
+            4,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FUSIONREPORT": {
+                    "fusion_report": "2.1.5"
+                },
+                "Workflow": {
+                    "nf-core/rnafusion": "v4.0.0dev"
+                }
+            },
+            [
+                "fastqc",
+                "fastqc/test.html",
+                "fastqc/test.zip",
+                "fusionreport",
+                "fusionreport/test",
+                "fusionreport/test/AAA_BBB.html",
+                "fusionreport/test/test.fusionreport.tsv",
+                "fusionreport/test/test.fusionreport_filtered.tsv",
+                "fusionreport/test/test.fusions.csv",
+                "fusionreport/test/test.fusions.json",
+                "fusionreport/test/test_fusionreport_index.html",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "salmon",
+                "salmon/test",
+                "salmon/test_lib_format_counts.json",
+                "salmon/test_meta_info.json"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-03T19:27:00.717876194"
+    },
+    "stub test with fastp trim": {
+        "content": [
+            6,
+            {
+                "FASTP": {
+                    "fastp": "0.23.4"
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "FASTQC_FOR_FASTP": {
+                    "fastqc": "0.12.1"
+                },
+                "FUSIONREPORT": {
+                    "fusion_report": "2.1.5"
+                },
+                "Workflow": {
+                    "nf-core/rnafusion": "v4.0.0dev"
+                }
+            },
+            [
+                "fastp",
+                "fastp/test.fastp.html",
+                "fastp/test.fastp.json",
+                "fastp/test.fastp.log",
+                "fastp/test_1.fastp.fastq.gz",
+                "fastp/test_2.fastp.fastq.gz",
+                "fastqc",
+                "fastqc/test.html",
+                "fastqc/test.zip",
+                "fastqc_for_fastp",
+                "fastqc_for_fastp/test_trimmed.html",
+                "fastqc_for_fastp/test_trimmed.zip",
+                "fusionreport",
+                "fusionreport/test",
+                "fusionreport/test/AAA_BBB.html",
+                "fusionreport/test/test.fusionreport.tsv",
+                "fusionreport/test/test.fusionreport_filtered.tsv",
+                "fusionreport/test/test.fusions.csv",
+                "fusionreport/test/test.fusions.json",
+                "fusionreport/test/test_fusionreport_index.html",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "salmon",
+                "salmon/test",
+                "salmon/test_lib_format_counts.json",
+                "salmon/test_meta_info.json"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-03T19:26:43.375635514"
+    }
+}
\ No newline at end of file
diff --git a/workflows/build_references.nf b/workflows/build_references.nf
index def3c162..4886a7bb 100644
--- a/workflows/build_references.nf
+++ b/workflows/build_references.nf
@@ -49,7 +49,10 @@ workflow BUILD_REFERENCES {
     GATK4_BEDTOINTERVALLIST(BEDOPS_CONVERT2BED.out.bed, GATK4_CREATESEQUENCEDICTIONARY.out.dict)
 
     GFFREAD(ENSEMBL_DOWNLOAD.out.gtf, ENSEMBL_DOWNLOAD.out.primary_assembly.map { meta, fasta -> [ fasta ] })
-    SALMON_INDEX(ENSEMBL_DOWNLOAD.out.primary_assembly.map{ meta, fasta -> [ fasta ] }, GFFREAD.out.gffread_fasta.map{ meta, gffread_fasta -> [ gffread_fasta ] })
+
+    if (!params.skip_salmon_index){
+        SALMON_INDEX(ENSEMBL_DOWNLOAD.out.primary_assembly.map{ meta, fasta -> [ fasta ] }, GFFREAD.out.gffread_fasta.map{ meta, gffread_fasta -> [ gffread_fasta ] })
+    }
 
     if (params.starindex || params.all || params.starfusion || params.arriba) {
         STAR_GENOMEGENERATE( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.gtf )