Set minimum mutations per sample threshold

bin/subset_maf.py

@@ -9,7 +9,7 @@
 from read_utils import custom_na_values
 
 
-def subset_mutation_dataframe(sample_name, mutations_file, mutations_file_out, json_filters, requested_fields):
+def subset_mutation_dataframe(sample_name, mutations_file, mutations_file_out, json_filters, requested_fields, minimum_mutations):
     """
     INFO
     """
@@ -43,6 +43,10 @@ def subset_mutation_dataframe(sample_name, mutations_file, mutations_file_out, j
     with open(requested_fields, 'r') as file:
         output_format = json.load(file)
 
+    if annotated_maf.shape[0] < minimum_mutations:
+        print(f"{mutations_file_out} file will not be written since it has not reached the minimum number of mutations required for per sample analysis")
+        return False
+
     if output_format:
         header_ = output_format.get("header", False)
         columns = output_format.get("columns", annotated_maf.columns.values)
@@ -73,11 +77,12 @@ def subset_mutation_dataframe(sample_name, mutations_file, mutations_file_out, j
 @click.option('--out_maf', type=click.Path(), help='Output MAF file')
 @click.option('--json_filters', type=click.Path(exists=True), help='Input mutation filtering criteria file')
 @click.option('--req_fields', type=click.Path(exists=True), help='Column names to output')
+@click.option('--min_mutations', type=int, default=-1, help='Minimum number of mutations for sample to be outputted.')
 # @click.option('--plot', is_flag=True, help='Generate plot and save as PDF')
 
-def main(sample_name, mut_file, out_maf, json_filters, req_fields): # , plot):
+def main(sample_name, mut_file, out_maf, json_filters, req_fields, min_mutations): # , plot):
     click.echo(f"Subsetting MAF file...")
-    subset_mutation_dataframe(sample_name, mut_file, out_maf, json_filters, req_fields)
+    subset_mutation_dataframe(sample_name, mut_file, out_maf, json_filters, req_fields, min_mutations)
 
 if __name__ == '__main__':
     main()

conf/modules.config

@@ -234,8 +234,9 @@ process {
     }
 
     withName: 'SOMATICMUTATIONS' {
-        ext.output_prefix = '.somatic'
-        ext.output_fmt  = { ['"header": true'].join(',\t').trim() }
+        ext.output_prefix       = '.somatic'
+        ext.output_fmt          = { ['"header": true'].join(',\t').trim() }
+        ext.minimum_mutations   = params.min_muts_per_sample
 
         publishDir       = [
             [

modules/local/subsetmaf/main.nf

@@ -9,8 +9,8 @@ process SUBSET_MAF {
     tuple val(meta), path(mut_files)
 
     output:
-    tuple val(meta), path("*.mutations.tsv")  , emit: mutations
-    path "versions.yml"                       , topic: versions
+    tuple val(meta), path("*.mutations.tsv")  , optional : true , emit: mutations
+    path "versions.yml"                                         , topic: versions
 
 
     script:
@@ -20,6 +20,7 @@ process SUBSET_MAF {
     def output_prefix = task.ext.output_prefix ?: ""
     def filters = task.ext.filters ?: ""
     def output_format = task.ext.output_fmt ?: ""
+    def min_muts = task.ext.minimum_mutations ? "--min_mutations ${task.ext.minimum_mutations}" : ""
     """
     cat > mutations_subset.conf << EOF
     {
@@ -39,6 +40,7 @@ process SUBSET_MAF {
                     --out_maf ${prefix}${output_prefix}.mutations.tsv \\
                     --json_filters mutations_subset.conf \\
                     --req_fields output_formats.conf \\
+                    ${min_muts} \\
                     ${args}
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

nextflow.config

@@ -85,7 +85,7 @@ params {
 
     regressions                 = false
 
-    filter_criteria             =  ["notcontains NM20", "notcontains p8", "notcontains n_rich", "notcontains cohort_n_rich_threshold", "notcontains cohort_n_rich", "notcontains no_pileup_support", "notcontains low_mappability", "notcontains not_covered" ]
+    filter_criteria             =  ["notcontains NM20", "notcontains n_rich", "notcontains cohort_n_rich_threshold", "notcontains cohort_n_rich", "notcontains no_pileup_support", "notcontains low_mappability", "notcontains not_covered" ]
     filter_criteria_somatic     =  []
     no_filter                   = false
 
@@ -94,6 +94,7 @@ params {
     sample_panel_min_depth      = 40
     consensus_panel_min_depth   = 500
     consensus_compliance        = 0.8
+    min_muts_per_sample        = 0
     selected_genes              = ''
     panel_with_canonical        = true
 

nextflow_schema.json

@@ -560,6 +560,12 @@
                     "fa_icon": "fas fa-book",
                     "help_text": ""
                 },
+                "min_muts_per_sample": {
+                    "type": "number",
+                    "description": "Threshold on minimum number of mutations that a sample needs to have for doing a per-sample analysis of that specific case",
+                    "fa_icon": "fas fa-book",
+                    "help_text": ""
+                },
                 "selected_genes": {
                     "type": "string",
                     "description": "Comma-separeted list of genes to focus the analysis",