changed minimac for the sav format

Author: psnehal

modules/local/imputation/minimac4.nf

@@ -20,6 +20,10 @@ process MINIMAC4 {
     tuple val(chr_cleaned), val(start), val(end), file("*.dose.vcf.gz"), file("*.info.gz"), file("*.empiricalDose.vcf.gz"), emit: imputed_chunks
 
     script:
+    output_format = params.imputation.output_format ?: 'vcf.gz'
+    if (!['sav', 'vcf.gz'].contains(output_format)) {
+            throw new IllegalArgumentException("Invalid params.imputation.output_format: ${output_format}. Use 'sav' or 'vcf.gz'.")
+        }
     map = minimac_map ? '--map ' + minimac_map : ''
     r2_filter = min_r2 != 0 ? '--min-r2 ' + min_r2 : ''
     diff_threshold = diffThreshold != -1 ? '--diff-threshold ' + diffThreshold : ''
@@ -31,19 +35,22 @@ process MINIMAC4 {
     chr_mapped = (refpanel_build == 'hg38') ? 'chr' + chr_cleaned : chr_cleaned
     used_threads = params.service.threads != -1 ? params.service.threads : task.cpus
 
+    dose_output = "${chunkfile_name}.dose.${output_format}"
+    empirical_output = "${chunkfile_name}.empiricalDose.${output_format}"
+
     """
     tabix ${chunkfile}
 
     minimac4 \
         --region ${chr_mapped}:${start}-${end} \
         --overlap ${minimac_window} \
-        --output ${chunkfile_name}.dose.vcf.gz \
-        --output-format vcf.gz \
+        --output ${dose_output} \
+        --output-format ${output_format} \
         --format GT,DS,GP,HDS \
         --min-ratio ${minimac_min_ratio} \
         --all-typed-sites \
         --sites ${chunkfile_name}.info.gz \
-        --empirical-output ${chunkfile_name}.empiricalDose.vcf.gz \
+        --empirical-output ${empirical_output} \
         --threads ${used_threads} \
         --decay ${decay} \
         --temp-prefix ./ \

nextflow.config

@@ -56,6 +56,7 @@ params {
         prob_threshold_s1 : -1,
         diff_threshold    : -1,
         min_recom         : -1,
+        output_format     : 'vcf.gz' #'either vcf.gz or sav'
     ]
 
     encryption = [