adjust pre-commit p1

caravagnalab · Dec 30, 2024 · 1e11d1f · 1e11d1f
1 parent 131b602
commit 1e11d1f
Show file tree

Hide file tree

Showing 55 changed files with 1,564 additions and 1,707 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -58,7 +58,6 @@ process {
     withLabel:error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
-
     }
 }
 
diff --git a/conf/modules/cnaqc.config b/conf/modules/cnaqc.config
@@ -1,10 +1,9 @@
 process {
     withName: 'CNAQC'{
-	memory = { check_max( 20.GB * task.attempt, 'memory' ) }
-	cpus = { check_max( 4 * task.attempt, 'cpus' ) }
-        time = { check_max( 4.h  * task.attempt, 'time'   ) }        
+        memory = { check_max( 20.GB * task.attempt, 'memory' ) }
+        cpus = { check_max( 4 * task.attempt, 'cpus' ) }
+        time = { check_max( 4.h  * task.attempt, 'time'   ) }
         errorStrategy = 'retry'
-
         publishDir = [
             [
                 mode: params.publish_dir_mode,

diff --git a/conf/modules/driver_annotation.config b/conf/modules/driver_annotation.config
@@ -1,59 +1,14 @@
-// FIXME ANNOTATE_DRIVER not used anymore
- process{
-     withName: 'ANNOTATE_DRIVER' {
-         memory = '15 GB'
-         time = '15 min'
-         errorStrategy = 'finish'
-         publishDir = [
-                 [
-                     mode: params.publish_dir_mode,
-                     path: { "${params.outdir}/driver_annotation/annotate_driver/${meta.dataset}/${meta.patient}/${meta.tumour_sample}/"},
-                     pattern: "*{rds}"
-                 ]
-             ]    
-     }
- }
-
- //process{
- //   withName: 'JOIN_ANNOTATION' {
- //        memory = '15 GB'
- //        time = '15 min'
- //        errorStrategy = 'finish'
- //        publishDir = [
- //                [
- //                    mode: params.publish_dir_mode,
- //                    path: { "${params.outdir}/driver_annotation/join_annotation/${meta.dataset}/${meta.patient}/${meta.tumour_sample}/"},
- //                    pattern: "*{rds}"
- //                ]
- //            ]    
- //    }
- //
- //}
-
-//process{
-//     withName: 'DNDSCV' {
-//         memory = '15 GB'
-//         time = '15 min'
-//         errorStrategy = 'ignore'
-//         publishDir = [
-//                 [
-//                     mode: params.publish_dir_mode,
-//                     path: { "${params.outdir}/driver_annotation/DNDSCV/${meta.dataset}/"},
-//                     pattern: "*{rds}"
-//                 ]
-//             ]    
-//     }
-
-//     withName: 'BUILD_REFERENCE' {
-//        memory = '10 GB'
-//         time = '20 min'
-//         errorStrategy = 'ignore'
-//         publishDir = [
-//                 [
-//                     mode: params.publish_dir_mode,
-//                     path: { "${params.outdir}/driver_annotation/BUILD_REFERENCE/"},
-//                     pattern: "*{rds}"
-//                 ]
-//             ]    
-//     }
-// }
+process{
+    withName: 'ANNOTATE_DRIVER' {
+        memory = '15 GB'
+        time = '15 min'
+        errorStrategy = 'finish'
+        publishDir = [
+                [
+                    mode: params.publish_dir_mode,
+                    path: { "${params.outdir}/driver_annotation/annotate_driver/${meta.dataset}/${meta.patient}/${meta.tumour_sample}/"},
+                    pattern: "*{rds}"
+                ]
+            ]
+    }
+}
diff --git a/conf/modules/formatter.config b/conf/modules/formatter.config
@@ -1,7 +1,7 @@
 process {
     withName: 'CNA_PROCESSING'{
         memory = { check_max( 20.GB * task.attempt, 'memory' ) }
-	cpus = { check_max( 4 * task.attempt, 'cpus' ) }
+        cpus = { check_max( 4 * task.attempt, 'cpus' ) }
         time = '30 min'
         errorStrategy = 'retry'
         publishDir = [
@@ -14,7 +14,7 @@ process {
     }
 
     withName: 'VCF_PROCESSING'{
-	    memory = { check_max( 20.GB * task.attempt, 'memory' ) } 
+        memory = { check_max( 20.GB * task.attempt, 'memory' ) }
         time = '30 min'
         errorStrategy = 'retry'
         ext.args = {[

diff --git a/conf/modules/lifter.config b/conf/modules/lifter.config
@@ -1,12 +1,12 @@
- process{
+process{
     withName: 'GET_POSITIONS_ALL' {
         publishDir = [
                 [
                     mode: params.publish_dir_mode,
                     path: { "${params.outdir}/lifter/positions/${meta.dataset}/${meta.patient}/"},
                     pattern: "*{rds}"
                 ]
-            ]    
+        ]
         memory = '10 GB'
         time = '10 min'
         errorStrategy = 'finish'
@@ -18,12 +18,12 @@
                     mode: params.publish_dir_mode,
                     path: { "${params.outdir}/lifter/positions/${meta.dataset}/${meta.patient}/"}
                 ]
-            ]    
+        ]
         memory = '10 GB'
         time = '10 min'
         errorStrategy = 'finish'
     }
-  
+
     withName: 'JOIN_POSITIONS' {
         publishDir = [
             [
@@ -37,11 +37,9 @@
         errorStrategy = 'finish'
     }
 
-
     withName: 'BCFTOOLS_MPILEUP' {
         ext.args = { "--annotate FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR --threads 36" }
         ext.args2  = { "-m --threads 36" }
-
         publishDir = [
             [
                 mode: params.publish_dir_mode,
@@ -50,4 +48,4 @@
             ]
         ]
     }
- }
+}
diff --git a/conf/modules/pyclonevi.config b/conf/modules/pyclonevi.config
@@ -15,7 +15,6 @@ process {
                 "density": params.pyclonevi_density,
                 "n_grid_point": params.pyclonevi_n_grid_point,
                 "n_restarts": params.pyclonevi_n_restarts
-                // "remove_tail": params.remove_tail 
             ]
         }
     }

diff --git a/conf/modules/sigprofiler.config b/conf/modules/sigprofiler.config
@@ -15,13 +15,12 @@ process {
 
 process {
     withName: 'SIGPROFILER' {
-	    memory = { check_max( 100.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 100.GB * task.attempt, 'memory' ) }
         time = { check_max( 12.h * task.attempt, 'time' ) }
         singularity.runOptions = '--writable-tmpfs'
         cpus = { check_max( 12 * task.attempt, 'cpus' ) }
         maxForks = 20
         errorStrategy = 'retry'
-
         ext.args = {
             [
                 "exome": params.sigprofiler_exome,

diff --git a/conf/modules/sparsesignatures.config b/conf/modules/sparsesignatures.config
@@ -25,8 +25,8 @@ process {
             [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/signature_deconvolution/SparseSignatures/${meta.id}/" },
-		pattern: "*{rds,pdf}"
+                pattern: "*{rds,pdf}"
             ]
         ]
     }
- }
+}
diff --git a/conf/modules/tinc.config b/conf/modules/tinc.config
@@ -1,24 +1,25 @@
-process {
-    withName: 'TINC'{
-        memory='16 GB'
-        cpus='4'
-        time='6h'
-        errorStrategy='finish'
-        ext.args = {[
-            "vaf_range_tumour" : params.tinc_vaf_range_tumour, 
-            "cutoff_miscalled_clonal" : params.tinc_cutoff_miscalled_clonal, 
-            "cutoff_lv_assignment" : params.tinc_cutoff_lv_assignment,
-            "N" : params.tinc_N, 
-            "fast" : params.tinc_fast,
-            "normal_contamination_level" : params.tinc_normal_contamination_lv
-        ]}
-
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/QC/tinc/${meta.dataset}/${meta.patient}/${meta.tumour_sample}/" },
-                pattern: "*{rds,pdf,csv}"
-            ]
-        ]
-    }
-}
+process {
+    withName: 'TINC'{
+        memory='16 GB'
+        cpus='4'
+        time='6h'
+        errorStrategy='finish'
+        ext.args = {[
+            "vaf_range_tumour" : params.tinc_vaf_range_tumour,
+            "cutoff_miscalled_clonal" : params.tinc_cutoff_miscalled_clonal,
+            "cutoff_lv_assignment" : params.tinc_cutoff_lv_assignment,
+            "N" : params.tinc_N,
+            "fast" : params.tinc_fast,
+            "normal_contamination_level" : params.tinc_normal_contamination_lv
+        ]}
+
+        publishDir = [
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/QC/tinc/${meta.dataset}/${meta.patient}/${meta.tumour_sample}/" },
+                pattern: "*{rds,pdf,csv}"
+            ]
+        ]
+    }
+}
+
diff --git a/conf/test.config b/conf/test.config
@@ -22,34 +22,34 @@ params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-  // Input data
-  // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-  // TODO nf-core: Give any required params for the test so that command line flags are not needed
- 
-  input = "https://github.com/nf-core/test-datasets/blob/tumourevo/data/test_samplesheet.csv"
-  
-  // Genome references
-  genome = "GRCh38"
-  fasta = "https://github.com/nf-core/test-datasets/tree/tumourevo/data/REF/FASTA/chr17_genome.fasta"
-  filter = false
-  
-  drivers_table = "https://github.com/nf-core/test-datasets/blob/tumourevo/data/DRIVER_ANNOTATION/ANNOTATE_DRIVER/Compendium_Cancer_Genes.tsv"
-
-  download_cache_vep = false
-  vep_cache = "https://github.com/nf-core/test-datasets/blob/tumourevo/data/REF/VEP/vep.tar.gz"
-
-  vep_genome = "GRCh38" 
-  vep_cache_version = "110" 
-  vep_species = "Homo_sapiens"
-
-  sparsesignatures_K = "2:3"
-  sparsesignatures_nmf_runs = "3"
-  sparsesignatures_iterations = "10"
-  sparsesignatures_max_iterations_lasso = "100"
-  sparsesignatures_cross_validation_repetitions = "10"
-  sparsesignatures_cross_validation_iterations = "5"
-  sparsesignatures_lambda_values_alpha = "c(0.00, 0.01)"
-  sparsesignatures_lambda_values_beta = "c(0.01, 0.05)"
- 
-  tools = "mobster,viber,pyclone-vi,sparsesignatures"
+// Input data
+// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
+// TODO nf-core: Give any required params for the test so that command line flags are not needed
+
+    input = "https://github.com/nf-core/test-datasets/blob/tumourevo/data/test_samplesheet.csv"
+
+    // Genome references
+    genome = "GRCh38"
+    fasta = "https://github.com/nf-core/test-datasets/tree/tumourevo/data/REF/FASTA/chr17_genome.fasta"
+    filter = false
+
+    drivers_table = "https://github.com/nf-core/test-datasets/blob/tumourevo/data/DRIVER_ANNOTATION/ANNOTATE_DRIVER/Compendium_Cancer_Genes.tsv"
+
+    download_cache_vep = false
+    vep_cache = "https://github.com/nf-core/test-datasets/blob/tumourevo/data/REF/VEP/vep.tar.gz"
+
+    vep_genome = "GRCh38"
+    vep_cache_version = "110"
+    vep_species = "Homo_sapiens"
+
+    sparsesignatures_K = "2:3"
+    sparsesignatures_nmf_runs = "3"
+    sparsesignatures_iterations = "10"
+    sparsesignatures_max_iterations_lasso = "100"
+    sparsesignatures_cross_validation_repetitions = "10"
+    sparsesignatures_cross_validation_iterations = "5"
+    sparsesignatures_lambda_values_alpha = "c(0.00, 0.01)"
+    sparsesignatures_lambda_values_beta = "c(0.01, 0.05)"
+
+    tools = "mobster,viber,pyclone-vi,sparsesignatures"
 }
diff --git a/docs/output.md b/docs/output.md
@@ -243,7 +243,7 @@ The results of this step are collected in `{pubslish_dir}/signature_deconvolutio
   - exposure RDS plot
 
 </details>
-  
+
 ### SigProfiler
 
 [SigProfiler](https://osf.io/t6j7u/wiki/home/) is a python framework that allows _de novo_ extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of `SigProfilerMatrixGenerator` and `SigProfilerPlotting`, seamlessly integrating with other `SigProfiler` tools.

diff --git a/main.nf b/main.nf
@@ -55,7 +55,7 @@ workflow NFCORE_TUMOUREVO {
         ensemblvep_info = Channel.of([ [ id:"${params.vep_cache_version}_${params.vep_genome}" ], params.vep_genome, params.vep_species, params.vep_cache_version ])
         DOWNLOAD_CACHE_VEP(ensemblvep_info)
         vep_cache = DOWNLOAD_CACHE_VEP.out.ensemblvep_cache.map{ meta, cache -> [ cache ] }
-        
+
     } else {
         if (params.vep_cache.endsWith("tar.gz")){
             path = params.vep_cache ? Channel.fromPath(params.vep_cache).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty()
@@ -75,7 +75,7 @@ workflow NFCORE_TUMOUREVO {
             vep_cache  = ANNOTATION_CACHE_INITIALISATION.out.ensemblvep_cache
         }
     }
-    
+
     TUMOUREVO (
         input,
         fasta,
@@ -108,4 +108,4 @@ workflow {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+*/