Skip phasing when not specified

genepi · Nov 17, 2023 · bead927 · bead927
1 parent 3a2cfef
commit bead927
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Showing 5 changed files with 22 additions and 16 deletions.
diff --git a/modules/local/phasing/beagle.nf b/modules/local/phasing/beagle.nf
@@ -3,7 +3,7 @@ process BEAGLE {
     tag "${chunkfile}"
 
     input:
-    tuple val(chr), path(bcf), val(start), val(end), val(phasing_status), path(chunkfile), val(snps), val(in_reference),  path(map_beagle)
+    tuple val(chr), path(bcf), val(start), val(end), val(phasing_status), path(chunkfile), path(map_beagle)
     val phasing_method
 
     output:

diff --git a/modules/local/phasing/eagle.nf b/modules/local/phasing/eagle.nf
@@ -3,7 +3,7 @@ process EAGLE {
     tag "${chunkfile}"
 
     input:
-    tuple val(chr), path(bcf), path(bcf_csi), val(start), val(end), val(phasing_status), path(chunkfile), val(snps), val(in_reference)
+    tuple val(chr), path(bcf), path(bcf_csi), val(start), val(end), val(phasing_status), path(chunkfile)
     path map_eagle
 
     output:

diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -78,6 +78,7 @@ nextflow_pipeline {
                 password = PASSWORD
                 refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap2-chr20/cloudgene.yaml"
                 output = "${outputDir}"
+                phasing = "no_phasing"
             }
         }
 
@@ -92,19 +93,15 @@ nextflow_pipeline {
             assert imputed_chr_20.exists()
             ZipFile zipFile = new ZipFile(imputed_chr_20, PASSWORD.toCharArray());
             zipFile.extractAll("${outputDir}");
-
-            //TODO: this is from imputationserver-utils.jar. How to include? use alternative?
-            /*VcfFile file = VcfFileUtil.load("${outputDir}/chr20.dose.vcf.gz", 100000000, false);
-
+            def file = path("${outputDir}/chr20.dose.vcf.gz").vcf
             assert file.getChromosome() == "20"
             assert file.getNoSamples() == 51;
             assert file.isPhased()
-            assert file.getNoSnps() == TOTAL_REFPANEL_CHR20_B37 + ONLY_IN_INPUT*/
-
+            assert file.getNoSnps() == TOTAL_REFPANEL_CHR20_B37 + ONLY_IN_INPUT
+            
             //check correct number of snps in info.gz file
-            //TODO: phasing executed every time, therefore ONLY_IN_INPUT is currently not available
-           // assert path("${outputDir}/chr20.info.gz").linesGzip.size() == 1 + TOTAL_REFPANEL_CHR20_B37 + ONLY_IN_INPUT
-            assert path("${outputDir}/chr20.info.gz").linesGzip.size() == 1 + TOTAL_REFPANEL_CHR20_B37
+            assert path("${outputDir}/chr20.info.gz").linesGzip.size() == 1 + TOTAL_REFPANEL_CHR20_B37 + ONLY_IN_INPUT
+
         }
 
     }

diff --git a/workflows/imputationserver.nf b/workflows/imputationserver.nf
@@ -51,17 +51,26 @@ workflow IMPUTATIONSERVER {
             INPUT_VALIDATION.out,
             legend_files_ch.collect()
         )
-        //TODO: add phasing only mode
+
         if ("${params.mode}" != 'qc-only') {
 
-            PHASING(
-                QUALITY_CONTROL.out.qc_metafiles
+            imputation_ch =  QUALITY_CONTROL.out.qc_metafiles
+
+            if ("${params.phasing}" != 'no_phasing') { 
+
+                PHASING(
+                    imputation_ch
             )
 
+            imputation_ch = PHASING.out.phased_ch
+
+            }
+
+
             if ("${params.mode}" == 'imputation') {
 
                 IMPUTATION(
-                    PHASING.out.phased_ch
+                    imputation_ch
                 )
 
                 ENCRYPTION(

diff --git a/workflows/quality_control.nf b/workflows/quality_control.nf
@@ -29,7 +29,7 @@ workflow QUALITY_CONTROL {
     chunks_csv_index
         .combine(chunks_vcf_index, by: 0)
         .map{
-            row-> tuple(row[1], row[2], row[3], row[4], file(row[8]), row[6], row[7])
+            row-> tuple(row[1], row[2], row[3], row[4], file(row[8]))
         }
         .set { metafiles_ch }