nf-core · MaximilianStammnitz · Mar 11, 2026 · Mar 10, 2026 · Mar 10, 2026 · Mar 10, 2026
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -78,7 +78,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.04.4"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/deepmutscan/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/deepmutscan/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/deepmutscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A525.04.4-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

diff --git a/modules/local/bamprocessing/bam_filter/environment.yml b/modules/local/bamprocessing/bam_filter/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::samtools=1.21
diff --git a/...es/local/bamprocessing/bamfilteringdms.nf → ...es/local/bamprocessing/bam_filter/main.nf b/...es/local/bamprocessing/bamfilteringdms.nf → ...es/local/bamprocessing/bam_filter/main.nf
diff --git a/modules/local/bamprocessing/premerge/environment.yml b/modules/local/bamprocessing/premerge/environment.yml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bwa=0.7.19
+  - bioconda::samtools=1.21
+  - bioconda::vsearch=2.30.0
diff --git a/modules/local/bamprocessing/premerge.nf → modules/local/bamprocessing/premerge/main.nf b/modules/local/bamprocessing/premerge.nf → modules/local/bamprocessing/premerge/main.nf
diff --git a/modules/local/dmsanalysis/aa_seq/environment.yml b/modules/local/dmsanalysis/aa_seq/environment.yml
@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-biostrings=2.74.0
+  - conda-forge::r-base=4.4.1
+  - conda-forge::r-biocmanager=1.30.25
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.5.1
+  - conda-forge::r-reshape2=1.4.4
+  - conda-forge::r-scales=1.3.0
+  - conda-forge::r-stringr=1.5.1
+  - conda-forge::r-tidyr=1.3.1
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-zoo=1.8_12
diff --git a/modules/local/dmsanalysis/aaseq.nf → modules/local/dmsanalysis/aa_seq/main.nf b/modules/local/dmsanalysis/aaseq.nf → modules/local/dmsanalysis/aa_seq/main.nf
diff --git a/modules/local/dmsanalysis/templates/aa_seq.R → ...cal/dmsanalysis/aa_seq/templates/aa_seq.R b/modules/local/dmsanalysis/templates/aa_seq.R → ...cal/dmsanalysis/aa_seq/templates/aa_seq.R
diff --git a/modules/local/dmsanalysis/possible_mutations/environment.yml b/modules/local/dmsanalysis/possible_mutations/environment.yml
@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-biostrings=2.74.0
+  - conda-forge::r-base=4.4.1
+  - conda-forge::r-biocmanager=1.30.25
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.5.1
+  - conda-forge::r-reshape2=1.4.4
+  - conda-forge::r-scales=1.3.0
+  - conda-forge::r-stringr=1.5.1
+  - conda-forge::r-tidyr=1.3.1
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-zoo=1.8_12
diff --git a/...es/local/dmsanalysis/possiblemutations.nf → ...al/dmsanalysis/possible_mutations/main.nf b/...es/local/dmsanalysis/possiblemutations.nf → ...al/dmsanalysis/possible_mutations/main.nf
diff --git a/...msanalysis/templates/possible_mutations.R → ..._mutations/templates/possible_mutations.R b/...msanalysis/templates/possible_mutations.R → ..._mutations/templates/possible_mutations.R
diff --git a/modules/local/dmsanalysis/process_gatk/environment.yml b/modules/local/dmsanalysis/process_gatk/environment.yml
@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-biostrings=2.74.0
+  - conda-forge::r-base=4.4.1
+  - conda-forge::r-biocmanager=1.30.25
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.5.1
+  - conda-forge::r-reshape2=1.4.4
+  - conda-forge::r-scales=1.3.0
+  - conda-forge::r-stringr=1.5.1
+  - conda-forge::r-tidyr=1.3.1
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-zoo=1.8_12
diff --git a/modules/local/dmsanalysis/processgatk.nf → ...es/local/dmsanalysis/process_gatk/main.nf b/modules/local/dmsanalysis/processgatk.nf → ...es/local/dmsanalysis/process_gatk/main.nf
diff --git a/...ocal/dmsanalysis/templates/process_gatk.R → ...sis/process_gatk/templates/process_gatk.R b/...ocal/dmsanalysis/templates/process_gatk.R → ...sis/process_gatk/templates/process_gatk.R
diff --git a/modules/local/fitness/find_synonymous_mutation/environment.yml b/modules/local/fitness/find_synonymous_mutation/environment.yml
@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-biostrings=2.74.0
+  - conda-forge::r-base=4.4.1
+  - conda-forge::r-biocmanager=1.30.25
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.5.1
+  - conda-forge::r-reshape2=1.4.4
+  - conda-forge::r-scales=1.3.0
+  - conda-forge::r-stringr=1.5.1
+  - conda-forge::r-tidyr=1.3.1
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-zoo=1.8_12
diff --git a/...local/fitness/find_synonymous_mutation.nf → .../fitness/find_synonymous_mutation/main.nf b/...local/fitness/find_synonymous_mutation.nf → .../fitness/find_synonymous_mutation/main.nf
diff --git a/...cal/fitness/templates/find_syn_mutation.R → ...us_mutation/templates/find_syn_mutation.R b/...cal/fitness/templates/find_syn_mutation.R → ...us_mutation/templates/find_syn_mutation.R
diff --git a/modules/local/fitness/fitness_QC/environment.yml b/modules/local/fitness/fitness_QC/environment.yml
@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-biostrings=2.74.0
+  - conda-forge::r-base=4.4.1
+  - conda-forge::r-biocmanager=1.30.25
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.5.1
+  - conda-forge::r-reshape2=1.4.4
+  - conda-forge::r-scales=1.3.0
+  - conda-forge::r-stringr=1.5.1
+  - conda-forge::r-tidyr=1.3.1
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-zoo=1.8_12
diff --git a/modules/local/fitness/fitness_QC/main.nf b/modules/local/fitness/fitness_QC/main.nf
@@ -0,0 +1,30 @@
+process FITNESS_QC {
+  tag { sample.sample }
+  label 'process_single'
+
+  conda "${moduleDir}/environment.yml"
+  container "${ workflow.containerEngine == 'singularity'
+      ? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
+      : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
+
+  input:
+    tuple val(sample), path(fitness_estimation_tsv)   // from FITNESS_CALCULATION
+
+  output:
+    tuple val(sample), path("fitness_estimation_count_correlation.pdf"), emit: counts_corr_pdf
+    tuple val(sample), path("fitness_estimation_fitness_correlation.pdf"), emit: fitness_corr_pdf
+    path "versions.yml", emit: versions
+
+  script:
+  template 'fitness_QC.R'
+
+  stub:
+  """
+    touch fitness_estimation_count_correlation.pdf
+    touch fitness_estimation_fitness_correlation.pdf
+    cat > versions.yml <<'EOF'
+    FITNESS_PLOTS:
+      stub-version: "0.0.0"
+    EOF
+  """
+}
diff --git a/modules/local/fitness/templates/fitness_QC.R → ...fitness/fitness_QC/templates/fitness_QC.R b/modules/local/fitness/templates/fitness_QC.R → ...fitness/fitness_QC/templates/fitness_QC.R
diff --git a/modules/local/fitness/fitness_calculation/environment.yml b/modules/local/fitness/fitness_calculation/environment.yml
@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-biostrings=2.74.0
+  - conda-forge::r-base=4.4.1
+  - conda-forge::r-biocmanager=1.30.25
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.5.1
+  - conda-forge::r-reshape2=1.4.4
+  - conda-forge::r-scales=1.3.0
+  - conda-forge::r-stringr=1.5.1
+  - conda-forge::r-tidyr=1.3.1
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-zoo=1.8_12
diff --git a/modules/local/fitness/fitness_calculation/main.nf b/modules/local/fitness/fitness_calculation/main.nf
@@ -0,0 +1,28 @@
+process FITNESS_CALCULATION {
+  tag { sample.sample }
+  label 'process_single'
+
+  conda "${moduleDir}/environment.yml"
+  container "${ workflow.containerEngine == 'singularity'
+      ? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
+      : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
+
+  input:
+    tuple val(sample), path(counts_merged)
+    path(exp_design)
+    path(syn_wt_txt)
+
+  output:
+    tuple val(sample), path("fitness_estimation.tsv"), emit: fitness_estimation
+    path "versions.yml", emit: versions
+
+  script:
+  template 'fitness_calculation.R'
+
+  stub:
+  """
+    touch fitness_estimation.tsv
+    echo "FITNESS_CALCULATION:" > versions.yml
+    echo "  stub-version: 0.0.0" >> versions.yml
+  """
+}
diff --git a/...l/fitness/templates/fitness_calculation.R → ...lculation/templates/fitness_calculation.R b/...l/fitness/templates/fitness_calculation.R → ...lculation/templates/fitness_calculation.R
diff --git a/modules/local/fitness/fitness_experimental_design/environment.yml b/modules/local/fitness/fitness_experimental_design/environment.yml
@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-biostrings=2.74.0
+  - conda-forge::r-base=4.4.1
+  - conda-forge::r-biocmanager=1.30.25
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.5.1
+  - conda-forge::r-reshape2=1.4.4
+  - conda-forge::r-scales=1.3.0
+  - conda-forge::r-stringr=1.5.1
+  - conda-forge::r-tidyr=1.3.1
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-zoo=1.8_12
diff --git a/...al/fitness/fitness_experimental_design.nf → ...tness/fitness_experimental_design/main.nf b/...al/fitness/fitness_experimental_design.nf → ...tness/fitness_experimental_design/main.nf
diff --git a/...ess/templates/dimsum_experimentalDesign.R → ...ign/templates/dimsum_experimentalDesign.R b/...ess/templates/dimsum_experimentalDesign.R → ...ign/templates/dimsum_experimentalDesign.R
diff --git a/modules/local/fitness/fitness_heatmap/environment.yml b/modules/local/fitness/fitness_heatmap/environment.yml
@@ -0,0 +1,15 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-biostrings=2.74.0
+  - conda-forge::r-base=4.4.1
+  - conda-forge::r-biocmanager=1.30.25
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.5.1
+  - conda-forge::r-reshape2=1.4.4
+  - conda-forge::r-scales=1.3.0
+  - conda-forge::r-stringr=1.5.1
+  - conda-forge::r-tidyr=1.3.1
+  - conda-forge::r-tidyverse=2.0.0
+  - conda-forge::r-zoo=1.8_12
diff --git a/modules/local/fitness/fitness_heatmap/main.nf b/modules/local/fitness/fitness_heatmap/main.nf
@@ -0,0 +1,29 @@
+process FITNESS_HEATMAP {
+  tag { sample.sample }
+  label 'process_single'
+
+  conda "${moduleDir}/environment.yml"
+  container "${ workflow.containerEngine == 'singularity'
+      ? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
+      : 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
+
+  input:
+    tuple val(sample), path(fitness_estimation_tsv)   // from FITNESS_CALCULATION
+    tuple val(sample), path(wt_seq)   		      // WT sequence
+
+  output:
+    tuple val(sample), path("fitness_heatmap.pdf"), emit: fitness_heatmap
+    path "versions.yml", emit: versions
+
+  script:
+    template 'fitness_heatmap.R'
+
+  stub:
+  """
+    touch fitness_heatmap.pdf
+    cat > versions.yml <<'EOF'
+    FITNESS_HEATMAP:
+      stub-version: "0.0.0"
+    EOF
+  """
+}
diff --git a/...local/fitness/templates/fitness_heatmap.R → ...tness_heatmap/templates/fitness_heatmap.R b/...local/fitness/templates/fitness_heatmap.R → ...tness_heatmap/templates/fitness_heatmap.R