adds option to keep hom-ref variants

README.md

@@ -84,6 +84,9 @@ nextflow run brwnj/smoove-nf -latest \
 + `--sexchroms`
 	+ Comma delimited names of the sex chromosome(s) used to infer sex, e.g. `--sexchroms 'chrX,chrY'`
 	+ **default:** 'X,Y'
++ `--homref`
+    + Keep hom-ref variants that are normally filtered when using `smoove genotype`
+    + **default:** false
 
 #### [covviz](https://github.com/brwnj/covviz) params
 + `--zthreshold`

main.nf

@@ -15,6 +15,7 @@ params.knownsites = false
 params.ped = false
 
 // variables
+homref = params.homref ?: false
 project = params.project ?: 'sites'
 sexchroms = params.sexchroms ?: 'X,Y'
 sexchroms = sexchroms.replaceAll(" ", "")
@@ -137,7 +138,10 @@ process smoove_genotype {
     file("${sample}-smoove.genotyped.vcf.gz") into genotyped_vcfs
 
     script:
+    include_homref = params.homref ? "export SMOOVE_KEEP_ALL=KEEP" : ""
     """
+    $include_homref
+
     wget -q https://raw.githubusercontent.com/samtools/samtools/develop/misc/seq_cache_populate.pl
     perl seq_cache_populate.pl -root \$(pwd)/cache $fasta 1> /dev/null 2> err || (cat err; exit 2)
     export REF_PATH=\$(pwd)/cache/%2s/%2s/%s:http://www.ebi.ac.uk/ena/cram/md5/%s

nextflow.config

@@ -8,6 +8,8 @@ params {
     zthreshold = 3.5
     distancethreshold = 150000
     slop = 500000
+    // true/false; true saves hom-ref variants in the VCF when genotyping
+    homref = false
 }
 
 process {
@@ -69,7 +71,7 @@ manifest {
     name = 'brwnj/smoove-nf'
     author = 'Joe Brown'
     description = "run smoove smoover and with additional QC packaged"
-    version = '1.0.3'
+    version = '1.0.4'
     nextflowVersion = '>=0.32.0'
     homePage = 'https://github.com/brwnj/smoove-nf'
     mainScript = 'main.nf'