Fixing minor bugs

nrhorner · Sep 6, 2023 · df59be1 · df59be1
1 parent 59847f7
commit df59be1
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Showing 3 changed files with 28 additions and 61 deletions.
diff --git a/conf/modules/filtering/maf_filtering.config b/conf/modules/filtering/maf_filtering.config
@@ -14,68 +14,35 @@
 // MAF FILTERING
 
 process {  // maf filtering
-    if (params.tools && params.tools.split(',').contains('filtering')) {
 
 
-		withName: "VCF2MAF" {
-            ext.args =  { [
-                "--inhibit-vep",
-                "--normal-id ${meta.normal_id}",
-                "--tumor-id ${meta.tumor_id}",
-                "--vcf-tumor-id ${meta.tumor_id}",
-                "--vcf-normal-id ${meta.normal_id}",
-                "--max-subpop-af 0.0001",
-                "--retain-ann gnomADg_AF,MAX_AF,MAX_AF_POPS",
-                "--retain-fmt AD,DP,AF,GT",
-                params.vep_genome              ? "--ncbi-build ${params.vep_genome}"              : '',
-                meta.variantcaller == "strelka"? "--vcf-tumor-id TUMOR --vcf-normal-id NORMAL"    : ''
-            ].join(' ').trim() }
-            ext.prefix     = { "${meta.id}.${meta.variantcaller}" }
-            publishDir       = [
+
+	withName: "MAF_FILTERING" {
+                ext.prefix = { "${meta.id}.filtered"}
+                ext.args   = { [params.whitelist? "--whitelist ${params.whitelist}": "",
+                                params.blacklist? "--blacklist ${params.blacklist}": ""].join(' ').trim() }
+                publishDir = [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/variants/annotated/unfiltered/${meta.patient}/${meta.id}/" },
+                path: { "${params.outdir}/variants/annotated/filtered/${meta.patient}/${meta.id}/" },
                 pattern: "*{maf,maf.gz}"
             ]
-        }
-
-		withName: "FILTERING" {
-	                ext.prefix = { "${meta.id}.filtered"}
-	                ext.args   = { [params.whitelist? "--whitelist ${params.whitelist}": "",
-	                                params.blacklist? "--blacklist ${params.blacklist}": ""].join(' ').trim() }
-	                publishDir = [
-	                mode: params.publish_dir_mode,
-	                path: { "${params.outdir}/variants/annotated/filtered/${meta.patient}/${meta.id}/" },
-	                pattern: "*{maf,maf.gz}"
-	            ]
-	    }
-
-	    withName: 'SAMTOOLS_MERGE_SECOND_PASS' {
-	            ext.prefix       = {"${meta.id}.merged_2ndpass"}
-	            publishDir       = [
-	                mode: params.publish_dir_mode,
-	                path: { "${params.outdir}/preprocessing/second_pass/input/${meta.patient}/${meta.id}/" },
-	                pattern: "*{bam}",
-	                enabled: params.save_align_intermeds
-	            ]
-	    }
+    }
 
+    withName: 'RNA_FILTERING' {
+            ext.prefix       = {"${meta.id}.rna_filt"}
+            ext.args   = { [params.rnaedits?       "--rnaedits ${params.rnaedits}": "",
+                            params.rna_pon?        "--pon   ${params.rna_pon}"    : "",
+                            params.chain?          "--chain ${params.chain}"      : "",
+                            params.fasta19?        "--ref19 ${params.fasta19}"    : "",
+                            params.rna_pon19?      "--pon19 ${params.rna_pon19}"  : ""
+                            ].join(' ').trim() }
 
+            publishDir       = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variants/annotated/filtered/${meta.patient}/${meta.id}/" },
+                pattern: "*{maf}",
+                enabled: true
+            ]
+    }
 
-	    withName: 'RNA_FILTERING' {
-	            ext.prefix       = {"${meta.id}.rna_filt"}
-	            ext.args   = { [params.rnaedits?       "--rnaedits ${params.rnaedits}": "",
-	                            params.rna_pon?        "--pon   ${params.rna_pon}"    : "",
-	                            params.chain?          "--chain ${params.chain}"      : "",
-	                            params.fasta19?        "--ref19 ${params.fasta19}"    : "",
-	                            params.rna_pon19?      "--pon19 ${params.rna_pon19}"  : ""
-	                            ].join(' ').trim() }
-
-	            publishDir       = [
-	                mode: params.publish_dir_mode,
-	                path: { "${params.outdir}/variants/annotated/filtered/${meta.patient}/${meta.id}/" },
-	                pattern: "*{maf}",
-	                enabled: true
-	            ]
-	    }
-	}
 }
diff --git a/subworkflows/local/maf_filtering/main.nf b/subworkflows/local/maf_filtering/main.nf
@@ -17,7 +17,7 @@ workflow MAF_FILTERING {
     maf       = Channel.empty()
     if (params.step in ['mapping', 'markduplicates', 'splitncigar',
                 'prepare_recalibration', 'recalibrate', 'variant_calling',
-                'normalise', 'consensus', 'filtering'] ) {
+                'normalise', 'consensus', 'filtering'] && (!(params.skip_tools && params.skip_tools.split(",").contains("filtering")))) {
 
         if (params.step == 'filtering') maf_to_filter = input_sample
 		maf_to_filter.dump(tag:"maf_to_filter")

diff --git a/subworkflows/local/vcf_consensus/main.nf b/subworkflows/local/vcf_consensus/main.nf
@@ -19,13 +19,13 @@ workflow VCF_CONSENSUS {
     main:
     versions             = Channel.empty()
 
-    maf_consensus_dna    = Channel.empty()
-    maf_consensus_rna    = Channel.empty()
-    mafs_status_dna      = Channel.empty()
+    maf_from_consensus_dna  = Channel.empty()
+    mafs_from_varcal_dna    = Channel.empty()
+    consensus_maf           = Channel.empty()
 
     if (params.step in ['mapping', 'markduplicates', 'splitncigar',
                         'prepare_recalibration', 'recalibrate', 'variant_calling',
-                        'normalise', 'consensus'] ) {
+                        'normalise', 'consensus'] && (!(params.skip_tools && params.skip_tools.split(",").contains("consensus")))) {
 
         if (params.step == 'consensus') vcf_to_consensus = input_sample
         // First we transform the maf to MAF