[DRAFT] Add GitHub Actions workflow for Nextflow linting

.github/workflows/main.yml

@@ -0,0 +1,44 @@
+name: Nextflow Lint and Auto-fix
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  lint:
+    name: Run Nextflow lint and commit fixes
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checkout the repo, full history needed to push
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.head_ref || github.ref_name }}
+
+      # Setup Nextflow
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2.0.0
+        with:
+          version: latest-stable
+
+      # Run Nextflow lint
+      - name: Run Nextflow lint
+        run: nextflow lint -format -harshil-alignment *
+
+      # Commit and push changes if any
+      - name: Commit and push lint auto-fixes
+        run: |
+          if [[ -n "$(git status --porcelain)" ]]; then
+            echo "Lint made changes, committing..."
+            git config user.name "github-actions[bot]"
+            git config user.email "github-actions[bot]@users.noreply.github.com"
+            git add -A
+            git commit -m "chore: apply Nextflow lint auto-fixes"
+            git push origin HEAD
+          else
+            echo "No changes to commit"
+          fi

conf/base.config

@@ -10,23 +10,23 @@
 
 process {
 
-    resourceLimits = [ cpus: params.max_cpus, memory: params.max_memory, time: params.max_time ]
+    resourceLimits = [cpus: params.max_cpus, memory: params.max_memory, time: params.max_time]
 
     // TODO nf-core: Check the defaults for all processes
-    cpus   = {  1                          }
-    memory = {  6.GB * task.attempt        }
-    time   = {  15.min  * task.attempt     }
+    cpus           = { 1 }
+    memory         = { 6.GB * task.attempt }
+    time           = { 15.min * task.attempt }
 
 
 
-    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
-    maxRetries    = 3
-    maxErrors     = '-1'
+    errorStrategy  = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries     = 3
+    maxErrors      = '-1'
 
-    withLabel:error_ignore {
+    withLabel: error_ignore {
         errorStrategy = 'ignore'
     }
-    withLabel:error_retry {
+    withLabel: error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
@@ -37,85 +37,84 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    withLabel:process_single {
-        cpus   = {  1                   }
+    withLabel: process_single {
+        cpus = { 1 }
     }
-    withLabel:process_low {
-        cpus   = {  2     * task.attempt }
-        memory = {  12.GB * task.attempt }
+    withLabel: process_low {
+        cpus   = { 2 * task.attempt }
+        memory = { 12.GB * task.attempt }
     }
-    withLabel:process_medium {
-        cpus   = {  6     * task.attempt }
-        memory = {  36.GB * task.attempt }
+    withLabel: process_medium {
+        cpus   = { 6 * task.attempt }
+        memory = { 36.GB * task.attempt }
     }
-    withLabel:process_high {
-        cpus   = {  12    * task.attempt }
-        memory = {  72.GB * task.attempt }
-        time   = {  16.h  * task.attempt }
+    withLabel: process_high {
+        cpus   = { 12 * task.attempt }
+        memory = { 72.GB * task.attempt }
+        time   = { 16.h * task.attempt }
     }
 
 
-    withLabel:process_low_memory {
-        memory = {  4.GB * task.attempt }
+    withLabel: process_low_memory {
+        memory = { 4.GB * task.attempt }
     }
-    withLabel:memory_medium {
-        memory = {  8.GB  * task.attempt }
+    withLabel: memory_medium {
+        memory = { 8.GB * task.attempt }
     }
-    withLabel:process_medium_high_memory {
-        memory = {  36.GB * task.attempt }
+    withLabel: process_medium_high_memory {
+        memory = { 36.GB * task.attempt }
     }
-    withLabel:process_high_memory {
-        memory = {  200.GB * task.attempt }
+    withLabel: process_high_memory {
+        memory = { 200.GB * task.attempt }
     }
 
 
 
-    withLabel:time_minimal {
-        time   = {  15.m  * task.attempt }
+    withLabel: time_minimal {
+        time = { 15.m * task.attempt }
     }
-    withLabel:time_low {
-        time   = {  4.h   * task.attempt }
+    withLabel: time_low {
+        time = { 4.h * task.attempt }
     }
-    withLabel:time_medium {
-        time   = {  8.h   * task.attempt }
+    withLabel: time_medium {
+        time = { 8.h * task.attempt }
     }
-    withLabel:process_long {
-        time   = {  20.h  * task.attempt }
+    withLabel: process_long {
+        time = { 20.h * task.attempt }
     }
 
 
 
-    withLabel:cpu_single_fixed {
-        cpus   = {  1                    }
+    withLabel: cpu_single_fixed {
+        cpus = { 1 }
     }
-    withLabel:cpu_single {
-        cpus   = {  1     * task.attempt }
+    withLabel: cpu_single {
+        cpus = { 1 * task.attempt }
     }
-    withLabel:process_low_fixed_cpus {
-        cpus   = {  2                     }
+    withLabel: process_low_fixed_cpus {
+        cpus = { 2 }
     }
-    withLabel:cpu_low {
-        cpus   = {  2     * task.attempt }
+    withLabel: cpu_low {
+        cpus = { 2 * task.attempt }
     }
-    withLabel:cpu_lowmed {
-        cpus   = {  4     * task.attempt }
+    withLabel: cpu_lowmed {
+        cpus = { 4 * task.attempt }
     }
-    withLabel:cpu_medium {
-        cpus   = {  8     * task.attempt }
+    withLabel: cpu_medium {
+        cpus = { 8 * task.attempt }
     }
-    withLabel:cpu_medium_high {
-        cpus   = {  12      }
+    withLabel: cpu_medium_high {
+        cpus = { 12 }
     }
-    withLabel:cpu_high {
-        cpus   = {  30    * task.attempt }
+    withLabel: cpu_high {
+        cpus = { 30 * task.attempt }
     }
-    withLabel:cpu_veryhigh {
-        cpus   = {  50    * task.attempt }
+    withLabel: cpu_veryhigh {
+        cpus = { 50 * task.attempt }
     }
 
 
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
-
 }

conf/general_files_BBG.config

@@ -1,30 +1,28 @@
 // This configuration file is used to define the general parameters for the pipeline when ran in BBGCluster
 params {
 
-    vep_cache               = "/workspace/datasets/vep"
+    vep_cache             = "/workspace/datasets/vep"
 
     // Fasta references
-    fasta                   = '/workspace/datasets/genomes/GRCh38/clean_n_fixed_genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.masked.fna'
+    fasta                 = '/workspace/datasets/genomes/GRCh38/clean_n_fixed_genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.masked.fna'
 
-    wgs_trinuc_counts       = "assets/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
+    wgs_trinuc_counts     = "assets/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
 
-    cosmic_ref_signatures   = "/workspace/datasets/transfer/ferriol_deepcsa/COSMIC_v3.4_SBS_GRCh38.txt"
-    wgs_trinuc_counts       = "/workspace/datasets/transfer/ferriol_deepcsa/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
-    cadd_scores             = "/workspace/datasets/CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz"
-    cadd_scores_ind         = "/workspace/datasets/CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz.tbi"
+    cosmic_ref_signatures = "/workspace/datasets/transfer/ferriol_deepcsa/COSMIC_v3.4_SBS_GRCh38.txt"
+    wgs_trinuc_counts     = "/workspace/datasets/transfer/ferriol_deepcsa/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
+    cadd_scores           = "/workspace/datasets/CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz"
+    cadd_scores_ind       = "/workspace/datasets/CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz.tbi"
 
-    dnds_ref_transcripts    = "/workspace/projects/prominent/analysis/dNdScv/data/reference_files/RefCDS_human_latest_intogen.rda"
-    dnds_covariates         = "/workspace/projects/prominent/analysis/dNdScv/data/reference_files/covariates_hg19_hg38_epigenome_pcawg.rda"
+    dnds_ref_transcripts  = "/workspace/projects/prominent/analysis/dNdScv/data/reference_files/RefCDS_human_latest_intogen.rda"
+    dnds_covariates       = "/workspace/projects/prominent/analysis/dNdScv/data/reference_files/covariates_hg19_hg38_epigenome_pcawg.rda"
 
     // oncodrive3d
-    datasets3d              = "/workspace/nobackup/scratch/oncodrive3d/datasets_240506"
-    annotations3d           = "/workspace/nobackup/scratch/oncodrive3d/annotations_240506"
-    domains_file            = "/workspace/projects/prominent/dev/internal_development/domains/o3d_pfam_parsed.tsv"
-
-
+    datasets3d            = "/workspace/nobackup/scratch/oncodrive3d/datasets_240506"
+    annotations3d         = "/workspace/nobackup/scratch/oncodrive3d/annotations_240506"
+    domains_file          = "/workspace/projects/prominent/dev/internal_development/domains/o3d_pfam_parsed.tsv"
 }
 
 
 // Define the cacheDir for the singularity images
-singularity.cacheDir        = '/workspace/datasets/pipelines/nextflow_containers'
-singularity.libraryDir      = '/workspace/datasets/pipelines/nextflow_containers'
+singularity.cacheDir = '/workspace/datasets/pipelines/nextflow_containers'
+singularity.libraryDir = '/workspace/datasets/pipelines/nextflow_containers'

conf/general_files_IRB.config

@@ -1,27 +1,25 @@
 // This configuration file is used to define the general parameters for the pipeline when ran in IRBCluster
 params {
 
-    vep_cache               = "/data/bbg/datasets/vep"
+    vep_cache             = "/data/bbg/datasets/vep"
 
     // Fasta references
-    fasta                   = '/data/bbg/datasets/genomes/GRCh38/clean_n_fixed_genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.masked.fna'
+    fasta                 = '/data/bbg/datasets/genomes/GRCh38/clean_n_fixed_genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.masked.fna'
 
-    wgs_trinuc_counts       = "assets/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
+    wgs_trinuc_counts     = "assets/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
 
-    cosmic_ref_signatures   = "/data/bbg/datasets/transfer/ferriol_deepcsa/COSMIC_v3.4_SBS_GRCh38.txt"
-    wgs_trinuc_counts       = "/data/bbg/datasets/transfer/ferriol_deepcsa/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
-    cadd_scores             = "/data/bbg/datasets/CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz"
-    cadd_scores_ind         = "/data/bbg/datasets/CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz.tbi"
+    cosmic_ref_signatures = "/data/bbg/datasets/transfer/ferriol_deepcsa/COSMIC_v3.4_SBS_GRCh38.txt"
+    wgs_trinuc_counts     = "/data/bbg/datasets/transfer/ferriol_deepcsa/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
+    cadd_scores           = "/data/bbg/datasets/CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz"
+    cadd_scores_ind       = "/data/bbg/datasets/CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz.tbi"
 
-    dnds_ref_transcripts    = "/data/bbg/projects/prominent/analysis/dNdScv/data/reference_files/RefCDS_human_latest_intogen.rda"
-    dnds_covariates         = "/data/bbg/projects/prominent/analysis/dNdScv/data/reference_files/covariates_hg19_hg38_epigenome_pcawg.rda"
+    dnds_ref_transcripts  = "/data/bbg/projects/prominent/analysis/dNdScv/data/reference_files/RefCDS_human_latest_intogen.rda"
+    dnds_covariates       = "/data/bbg/projects/prominent/analysis/dNdScv/data/reference_files/covariates_hg19_hg38_epigenome_pcawg.rda"
 
     // oncodrive3d
-    datasets3d              = "/data/bbg/nobackup/scratch/oncodrive3d/datasets_240506"
-    annotations3d           = "/data/bbg/nobackup/scratch/oncodrive3d/annotations_240506"
-    domains_file            = "/data/bbg/projects/prominent/dev/internal_development/domains/o3d_pfam_parsed.tsv"
-
-
+    datasets3d            = "/data/bbg/nobackup/scratch/oncodrive3d/datasets_240506"
+    annotations3d         = "/data/bbg/nobackup/scratch/oncodrive3d/annotations_240506"
+    domains_file          = "/data/bbg/projects/prominent/dev/internal_development/domains/o3d_pfam_parsed.tsv"
 }
 
 

conf/local.config

@@ -10,6 +10,5 @@
 ----------------------------------------------------------------------------------------
 */
 
-process.resourceLimits = [ cpus: 16, memory: 70.GB, time: 6.h ]
+process.resourceLimits = [cpus: 16, memory: 70.GB, time: 6.h]
 process.errorStrategy = 'finish'
-

conf/mice.config

@@ -3,37 +3,38 @@ params {
     config_profile_description = 'Running deepCSA for mice data'
 
     // Input data
-    input  = '/data/bbg/nobackup2/prominent/ucsf_mice/deepUMIcaller/deepCSA_input.med.csv'
+    input                      = '/data/bbg/nobackup2/prominent/ucsf_mice/deepUMIcaller/deepCSA_input.med.csv'
 
     // Fasta references
-    fasta = '/data/bbg/datasets/genomes/mm39/GCA_000001635.9_genome/GCA_000001635.9_GRCm39_genomic.fna'
+    fasta                      = '/data/bbg/datasets/genomes/mm39/GCA_000001635.9_genome/GCA_000001635.9_GRCm39_genomic.fna'
 
-    features_table           = "/data/bbg/nobackup2/prominent/ucsf_mice/2024-10-17_clinical_features_summary.tsv"
-    features_table_separator =  'tab'
-    features_table_dict      = ['"unique_identifier" : "sample"',
-                                    '"groups_of_interest" : [ ["DMBA"], ["TPA"], ["treatment"], ["sex"], ["timepoint"], ["timepoint", "treatment"], ["timepoint", "TPA"], ["timepoint", "DMBA"] ]'
-                                    ].join(',\t').trim()
+    features_table             = "/data/bbg/nobackup2/prominent/ucsf_mice/2024-10-17_clinical_features_summary.tsv"
+    features_table_separator   = 'tab'
+    features_table_dict        = [
+        '"unique_identifier" : "sample"',
+        '"groups_of_interest" : [ ["DMBA"], ["TPA"], ["treatment"], ["sex"], ["timepoint"], ["timepoint", "treatment"], ["timepoint", "TPA"], ["timepoint", "DMBA"] ]',
+    ].join(',\t').trim()
 
-    use_custom_minimum_depth    = 30
+    use_custom_minimum_depth   = 30
 
 
-    wgs_trinuc_counts   = "$projectDir/assets/trinucleotide_counts/trinuc_counts.mus_musculus.mm39.tsv"
+    wgs_trinuc_counts          = "${projectDir}/assets/trinucleotide_counts/trinuc_counts.mus_musculus.mm39.tsv"
 
-    vep_genome          = "GRCm39"
-    vep_cache_version   = 111
-    vep_out_format      = "tab"
-    vep_params          = "--no_stats --cache --offline --symbol --protein --canonical"
-    vep_species         = "mus_musculus"
-    vep_cache           = "/data/bbg/datasets/vep/mus_musculus/111_GRCm39"
+    vep_genome                 = "GRCm39"
+    vep_cache_version          = 111
+    vep_out_format             = "tab"
+    vep_params                 = "--no_stats --cache --offline --symbol --protein --canonical"
+    vep_species                = "mus_musculus"
+    vep_cache                  = "/data/bbg/datasets/vep/mus_musculus/111_GRCm39"
 
 
     // oncodrive3d
     datasets3d                 = "/data/bbg/nobackup/scratch/oncodrive3d/datasets_mouse"
     // annotations3d              = "/workspace/nobackup/scratch/oncodrive3d/annotations_240506"
 
-    omega_withingene              = false
-    omega_subgenic_bedfile      = "/data/bbg/datasets/transfer/ferriol_deepcsa/mouse_skin_panel.hotspots.bed4.bed"
-    hotspot_expansion           = 15
+    omega_withingene           = false
+    omega_subgenic_bedfile     = "/data/bbg/datasets/transfer/ferriol_deepcsa/mouse_skin_panel.hotspots.bed4.bed"
+    hotspot_expansion          = 15
 
 
     oncodrivefml               = false
@@ -50,8 +51,8 @@ params {
 
 
     signatures                 = true
-    mutationdensity               = true
-    mutated_cells_vaf     = false
+    mutationdensity            = true
+    mutated_cells_vaf          = false
 
     indels                     = false
 
@@ -75,12 +76,11 @@ params {
     mutation_depth_threshold   = 40
 
     repetitive_variant_thres   = 5
-
 }
 
 
 process {
-    withLabel:process_high_memory {
-        memory = {  15.GB * task.attempt }
+    withLabel: process_high_memory {
+        memory = { 15.GB * task.attempt }
     }
 }

conf/modes/basic.config

@@ -1,5 +1,5 @@
 params {
-    plot_depths   = true
-    signatures    = true
-    profileall    = true
+    plot_depths = true
+    signatures  = true
+    profileall  = true
 }