Remove phasing-only mode (#10)

genepi · Nov 21, 2023 · c71eee1 · c71eee1
1 parent c26720f
commit c71eee1
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Showing 7 changed files with 5 additions and 51 deletions.
diff --git a/cloudgene.yaml b/cloudgene.yaml
@@ -88,7 +88,6 @@ workflow:
       values:
         qconly: Quality Control Only
         imputation: Quality Control & Imputation
-        phasing: Quality Control & Phasing Only
 
     - id: aesEncryption
       description: AES 256 encryption

diff --git a/modules/local/compression/compression_encryption_vcf.nf b/modules/local/compression/compression_encryption_vcf.nf
@@ -23,23 +23,16 @@ process COMPRESSION_ENCRYPTION_VCF {
     def info_name = "${prefix}.info"
     def aes = params.encryption.aes ? "-mem=AES256" : ""
     def panel_version = RefPanelUtil.loadFromFile(params.refpanel_yaml).id
-    def phasing_version = "no_phasing"
-    switch(params.phasing) { 
-        case "eagle":  phasing_version ="${params.eagle_version}"; break;
-        case "beagle": phasing_version ="${params.beagle_version}"; break;
-    }
 
     """  
     # concat info files 
     csvtk concat ${info_joined} > ${info_name}
     bgzip ${info_name}
     
     # concat dosage files and update header 
-    # TODO: a new file is written with the new header, should we add this on a chunk level and ove this block to imputation module and re-header there?
     bcftools concat -n ${imputed_joined} -o tmp_${imputed_name} -Oz
     echo "##mis_pipeline=${params.pipeline_version}" > add_header.txt
-    echo "##mis_imputation=${params.imputation_version}" >> add_header.txt
-    echo "##mis_phasing=${phasing_version}" >> add_header.txt
+    echo "##mis_phasing=${params.phasing}" >> add_header.txt
     echo "##mis_panel=${panel_version}" >> add_header.txt
     bcftools annotate -h add_header.txt tmp_${imputed_name} -o ${imputed_name} -Oz
     rm tmp_${imputed_name}

diff --git a/nextflow.config b/nextflow.config
@@ -56,9 +56,6 @@ params {
     r2Filter               = 0
     password               = null
     pipeline_version       = 'michigan-imputationserver-1.6.0-rc5'
-    eagle_version          = 'eagle-2.4'
-    beagle_version         = 'beagle.18May20.d20.jar'
-    imputation_version     = 'minimac4-1.0.2'
 
     config = [
         send_mail: false

diff --git a/tests/input/chr20-unphased/chr20.R50.merged.1.330k.recode.unphased.small.vcf.gz b/tests/input/chr20-unphased/chr20.R50.merged.1.330k.recode.unphased.small.vcf.gz
diff --git a/tests/input/chr20-unphased/chr20.R50.merged.1.330k.recode.unphased.small.vcf.gz.tbi b/tests/input/chr20-unphased/chr20.R50.merged.1.330k.recode.unphased.small.vcf.gz.tbi
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -279,45 +279,10 @@ nextflow_pipeline {
 
             def header = getVcfHeader(path("${outputDir}/chr20.dose.vcf.gz"))
             assert header.getOtherHeaderLine("mis_phasing").getValue() == params.phasing
-            assert header.getOtherHeaderLine("mis_imputation").getKey()
             assert header.getOtherHeaderLine("mis_pipeline").getKey()
             assert header.getOtherHeaderLine("mis_panel").getKey()
         }
 
     }
-
-    test("Should run phasing-only") {
-
-        when {
-            params {
-                project  = "test-job"
-                build = "hg19"
-                files = "$projectDir/tests/input/chr20-phased/*.vcf.gz"
-                population = "eur"
-                mode = "phasing_only"
-                password = PASSWORD
-                refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap2-chr20/cloudgene.yaml"
-                output = "${outputDir}"
-            }
-        }
-
-        then {
-            assert workflow.success
-
-            def quality_control_log = file("${outputDir}/cloudgene.report.json")
-            assert quality_control_log.exists()
-            assert quality_control_log.text.contains("Remaining sites in total: 7,735")
-
-            //TODO: add phasing only mode in workflow!
-            //def imputed_chr_20 = file("${outputDir}/chr_20.zip");
-            //assert imputed_chr_20.exists()
-            //ZipFile zipFile = new ZipFile(imputed_chr_20, PASSWORD.toCharArray());
-            //zipFile.extractAll("${outputDir}");
-
-
-
-        }
-
-    }
 
 }
diff --git a/workflows/imputationserver.nf b/workflows/imputationserver.nf
@@ -59,23 +59,23 @@ workflow IMPUTATIONSERVER {
 
         if (params.mode != 'qc-only') {
 
-            imputation_ch =  QUALITY_CONTROL.out.qc_metafiles
+            phased_ch =  QUALITY_CONTROL.out.qc_metafiles
 
             if (params.phasing != 'no_phasing') { 
 
                 PHASING(
-                    imputation_ch
+                    QUALITY_CONTROL.out.qc_metafiles
                 )
 
-                imputation_ch = PHASING.out.phased_ch
+                phased_ch = PHASING.out.phased_ch
 
             }
 
 
             if (params.mode == 'imputation') {
 
                 IMPUTATION(
-                    imputation_ch
+                    phased_ch
                 )
 
                 ENCRYPTION(