369 add ID signatures in sigprofilerassignment

conf/modules.config

@@ -574,6 +574,17 @@ process {
             ]
         ]
     }
+
+    withName: SIGPROFILERASSIGNMENTINDELS {
+        ext.context_type = "ID" // define context as ID only when running with this call of the module
+        publishDir = [
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/signatures/sigprofilerassignment" },
+                pattern: "**{txt,pdf}",
+            ]
+        ]
+    }
 
     withName: HDPREASSIGNMENT {
         publishDir = [

modules/local/signatures/sigprofiler/assignment/cosmic_fit/main.nf

@@ -16,23 +16,26 @@ process SIGPROFILERASSIGNMENT_COSMIC_FIT {
 
 
     script:
-    def name = "${meta.id}.${type}"
     def assembly = task.ext.genome_assembly ?: "GRCh38"
-
+    def context_type = task.ext.context_type ?: "96" // "96", "288", "1536", "DINUC", and "ID"
+    def name = "${meta.id}.${type}.${context_type}"
+
     // FIXME: the definition of subgroups to exclude seems not to work in the new CLI SigProfilerAssignment
     // def exclude_signature_subgroups = params.exclude_subgroups ? "--exclude_signature_subgroups \"${params.exclude_subgroups}\"" : ""
+    // The default input format is "matrix".
     """
     mkdir -p spa_volume
     export SIGPROFILERMATRIXGENERATOR_VOLUME='./spa_volume'
     export SIGPROFILERPLOTTING_VOLUME='./spa_volume'
     export SIGPROFILERASSIGNMENT_VOLUME='./spa_volume'
 
     SigProfilerAssignment cosmic_fit \\
-            ${matrix} \\
+            ${matrix} \\    
             output_${name} \\
             --signature_database ${reference_signatures} \\
             --genome_build ${assembly} \\
             --cpu ${task.cpus} \\
+            --context_type ${context_type} \\
             --volume spa_volume
 
     cp output_${name}/Assignment_Solution/Activities/Decomposed_MutationType_Probabilities.txt output_${name}/Assignment_Solution/Activities/Decomposed_MutationType_Probabilities.${name}.txt;

modules/local/signatures/sigprofiler/matrixgenerator/main.nf

@@ -9,6 +9,7 @@ process SIGPROFILER_MATRIXGENERATOR {
 
     output:
     path("**plots/*"), optional : true, emit: output_plots
+    path("**ID/*ID83*"), optional : true, emit: matrix_ID83
     path("**ID/*")   , optional : true, emit: matrices_ID
     path("**DBS/*")  , optional : true, emit: matrices_DBS
     path("**SBS/*")  , optional : true, emit: matrices_SBS

nextflow.config

@@ -115,6 +115,7 @@ params {
 
 
     cosmic_ref_signatures                    = "COSMIC_v3.4_SBS_GRCh38.txt"
+    indel_ref_signatures                     = "COSMIC_v3.4_ID_GRCh37.txt" // note that for IDs it has been defined in the GRCh37 genome version
     wgs_trinuc_counts                        = "assets/trinucleotide_counts/trinuc_counts.homo_sapiens.tsv"
     cadd_scores                              = "CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz"
     cadd_scores_ind                          = "CADD/v1.7/hg38/whole_genome_SNVs.tsv.gz.tbi"

nextflow_schema.json

@@ -729,6 +729,15 @@
                     "fa_icon": "far fa-file-code",
                     "default": "COSMIC_v3.4_SBS_GRCh38.txt"
                 },
+                "indel_ref_signatures": {
+                    "type": "string",
+                    "format": "file-path",
+                    "mimetype": "text/plain",
+                    "description": "Path to file containing the reference indel (ID) signatures to use in SigProfilerAssignment.",
+                    "help_text": "You can obtain it from COSMIC website. Note that for ID signatures the GRCh37 genome version is used.",
+                    "fa_icon": "far fa-file-code",
+                    "default": "COSMIC_v3.4_ID_GRCh37.txt"
+                },
                 "wgs_trinuc_counts": {
                     "type": "string",
                     "format": "file-path",

workflows/deepcsa.nf

@@ -112,6 +112,7 @@ include { DNA_2_PROTEIN_MAPPING         as DNA2PROTEINMAPPING       } from '../m
 
 include { MAF_2_VCF                     as MAF2VCF                  } from '../modules/local/maf2vcf/main'
 include { SIGPROFILER_MATRIXGENERATOR   as SIGPROMATRIXGENERATOR    } from '../modules/local/signatures/sigprofiler/matrixgenerator/main'
+include { SIGPROFILERASSIGNMENT_COSMIC_FIT      as SIGPROFILERASSIGNMENTINDELS    } from '../modules/local/signatures/sigprofiler/assignment/cosmic_fit/main'
 
 include { MUTATIONS_2_SIGNATURES        as MUTS2SIGS                } from '../modules/local/mutations2sbs/main'
 
@@ -121,7 +122,7 @@ include { MUTATIONS_2_SIGNATURES        as MUTS2SIGS                } from '../m
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-workflow DEEPCSA{
+workflow DEEPCSA {
 
     // // Input channel definitions
     features_table  = channel.fromPath( params.features_table ?: params.input, checkIfExists: true)
@@ -132,6 +133,11 @@ workflow DEEPCSA{
     cosmic_ref      = params.cosmic_ref_signatures
                             ? channel.fromPath( params.cosmic_ref_signatures, checkIfExists: true).first()
                             : channel.empty()
+    cosmic_indel_ref   = params.indel_ref_signatures
+                            ? channel.fromPath( params.indel_ref_signatures, checkIfExists: true).first()
+                            : channel.empty()
+
+
     datasets3d      = params.datasets3d
                             ? channel.fromPath( params.datasets3d, checkIfExists: true).first()
                             : channel.empty()
@@ -547,8 +553,16 @@ workflow DEEPCSA{
         vcf_files = MAF2VCF.out.vcf_files.flatten().collect()
 
         SIGPROMATRIXGENERATOR(
-            vcf_files,
-            )
+            vcf_files)
+
+         // --> external arg 
+
+        SIGPROMATRIXGENERATOR.out.matrix_ID83
+        .map{ it -> [ [id:"all_samples"], "indels", it] }
+        .set{ indels_matrix }
+
+        SIGPROFILERASSIGNMENTINDELS(indels_matrix, cosmic_indel_ref)
+    }
 
         // Signature Analysis
         if (params.profileall){