adding filtering

mop_dna/mop_dna.nf

@@ -37,6 +37,7 @@ pars_tools                              : ${params.pars_tools}
 clairS                                  : ${params.clairS}
 sniffles                                : ${params.sniffles}
 ***************************************************************
+filter                                  : ${params.filter}
 annotation                              : ${params.annotation}
 email                                   : ${params.email}
 """
@@ -57,9 +58,6 @@ evaluate(new File("../outdirs.nf"))
 def local_modules = file("$baseDir/../local_modules.nf")
 def subworkflowsDir = "${baseDir}/../BioNextflow/subworkflows"
 
-def flows = [:]
-flows["clairS"] = params.clairS
-
 include { getParameters; mapIDPairs } from "${local_modules}"
 include { final_message; notify_slack } from "${subworkflowsDir}/global_functions.nf"
 include { checkRef } from "${local_modules}"
@@ -73,6 +71,7 @@ include { FAIDX as SAMTOOLS_FAIDX } from "${subworkflowsDir}/misc/samtools"
 include { RUN as RUN_SNIFFLES } from "${subworkflowsDir}/structural_variant/sniffles.nf" addParams(EXTRAPARS: progPars["sniffles--sniffles"], OUTPUT:outputSniffles, LABEL:'big_mem_cpus', CONTAINER:'quay.io/biocontainers/sniffles:2.3.3--pyhdfd78af_0')
 include { RUN_MULTI as RUN_MULTI_SNIFFLES }  from "${subworkflowsDir}/structural_variant/sniffles.nf" addParams(EXTRAPARS: progPars["sniffles_multi--sniffles"], OUTPUT:outputSniffles, LABEL:'big_mem_cpus', CONTAINER:'quay.io/biocontainers/sniffles:2.3.3--pyhdfd78af_0')
 include { ANN as SNPEFF_ANN }  from "${subworkflowsDir}/var_annotation/snpeff.nf" addParams(EXTRAPARS: progPars["commong--snpEff"], OUTPUT:outputAnnotation)
+include { VIEW as BCFTOOLS_VIEW }  from "${subworkflowsDir}/snp_calling/bcftools.nf" addParams(EXTRAPARS: progPars["filter--bcftools-view"], OUTPUT:outputFiltered)
 include { REPORT as MULTIQC } from "${subworkflowsDir}/reporting/multiqc" addParams(OUTPUT:outputMultiQC)
 
 
@@ -137,8 +136,11 @@ workflow {
     }
 
     all_vcf = vcf_clairS.mix(vcf_sniffles)
+	if (params.filter != "NO") {
+		filt_vcf = BCFTOOLS_VIEW(all_vcf)
+	}
 
-    annos = SNPEFF_ANN(all_vcf, params.snpeff_db, snpEff_data, snpEff_config).csv_summary.map{it[1]}
+    annos = SNPEFF_ANN(filt_vcf, params.snpeff_db, snpEff_data, snpEff_config).csv_summary.map{it[1]}
 
 	MULTIQC(annos.collect())
 }

mop_dna/params.yaml

@@ -10,6 +10,7 @@ pars_tools: "${projectDir}/tools_opt.tsv"
 # flows
 clairS: "YES"
 sniffles: "YES"
+filter: "YES"
 annotation: "YES"
 
 # epinano plots

mop_dna/tools_opt.tsv

@@ -2,4 +2,5 @@
 sniffles	sniffles	"--tandem-repeats ${projectDir}/anno/human_GRCh38_no_alt_analysis_set.trf.bed"
 sniffles_multi	sniffles	""
 clairS	clairS	"-p ont_r9_guppy"
+filter	bcftools-view	"-f PASS"
 common	snpEff	""	

outdirs.nf

@@ -21,6 +21,8 @@ outputModPhredFlow   = "${params.output}/modphred_flow"
 outputClairS         = "${params.output}/clairS_flow"
 outputSniffles       = "${params.output}/sniffles_flow"
 outputAnnotation     = "${params.output}/annotation"
+outputFiltered       = "${params.output}/filtered_vcf"
+
 // MOP_TAIL
 outputTailFindr     = "${params.output}/tailfindr_flow"
 outputNanopolish    = "${params.output}/nanopolish_flow"