seppinho · Sep 29, 2025 · Sep 29, 2025 · Sep 29, 2025 · Sep 29, 2025 · Sep 29, 2025
diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -24,7 +24,7 @@ jobs:
       - name: Setup Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
-          version: "latest-edge"
+          version: "latest-stable"
 
       - name: Install nf-test
         run: |

diff --git a/modules/local/qc_filter_genotyped.nf b/modules/local/qc_filter_genotyped.nf
@@ -4,6 +4,7 @@ process QC_FILTER_GENOTYPED {
 
     input:
     tuple val(genotyped_plink_filename), path(genotyped_plink_file)
+    path phenotypes_file
 
     output:
     path "${genotyped_plink_filename}.qc.log"
@@ -15,6 +16,7 @@ process QC_FILTER_GENOTYPED {
     """
     plink2 \
         --bfile ${genotyped_plink_filename} \
+        --keep ${phenotypes_file} \
         --maf ${params.qc_maf} \
         --mac ${params.qc_mac} \
         --geno ${params.qc_geno} \

diff --git a/nextflow.config b/nextflow.config
@@ -126,7 +126,6 @@ profiles {
 
     docker {
         docker.enabled                    = true
-        docker.userEmulation              = true
         singularity.enabled               = false
     }
 
@@ -139,7 +138,6 @@ profiles {
     development {
         process.container                 = 'genepi/nf-gwas:latest'
         docker.enabled                    = true
-        docker.userEmulation              = true
         resume                            = true
         singularity.enabled               = false
     }

diff --git a/tests/modules/local/qc_filter_genotyped.nf.test b/tests/modules/local/qc_filter_genotyped.nf.test
@@ -11,6 +11,7 @@ nextflow_process {
             process {
                 """
                  input[0] =  Channel.fromFilePairs("$projectDir/tests/input/pipeline/example.{bim,bed,fam}", size: 3)
+                 input[1] = file("$projectDir/tests/input/pipeline/phenotype.txt")
                 """
             }
         }

diff --git a/workflows/gene_based_tests.nf b/workflows/gene_based_tests.nf
@@ -66,7 +66,7 @@ workflow GENE_BASED_TESTS {
 
     if (!skip_predictions) {
 
-        QUALITY_CONTROL(genotyped_plink_ch)
+        QUALITY_CONTROL(genotyped_plink_ch, phenotypes_file_validated)
         genotyped_final_ch = QUALITY_CONTROL.out.genotyped_filtered_files_ch
         genotyped_filtered_snplist_ch = QUALITY_CONTROL.out.genotyped_filtered_snplist_ch
         genotyped_filtered_id_ch = QUALITY_CONTROL.out.genotyped_filtered_id_ch

diff --git a/workflows/quality_control.nf b/workflows/quality_control.nf
@@ -3,12 +3,14 @@ include { QC_FILTER_GENOTYPED } from '../modules/local/qc_filter_genotyped'
 workflow QUALITY_CONTROL {
 
     take:
-    genotyped_plink_ch    
+    genotyped_plink_ch
+    phenotypes_file_validated    
 
     main:
 
     QC_FILTER_GENOTYPED (
-        genotyped_plink_ch
+        genotyped_plink_ch,
+        phenotypes_file_validated
     )
 
     emit: 

diff --git a/workflows/single_variant_tests.nf b/workflows/single_variant_tests.nf
@@ -58,7 +58,7 @@ workflow SINGLE_VARIANT_TESTS {
 
     if (!skip_predictions) {
 
-        QUALITY_CONTROL(genotyped_plink_ch)
+        QUALITY_CONTROL(genotyped_plink_ch, phenotypes_file_validated)
         genotyped_final_ch = QUALITY_CONTROL.out.genotyped_filtered_files_ch
         genotyped_filtered_snplist_ch = QUALITY_CONTROL.out.genotyped_filtered_snplist_ch
         genotyped_filtered_id_ch = QUALITY_CONTROL.out.genotyped_filtered_id_ch
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ nextflow_process { @@
                 process {
                     """
                      input[0] =  Channel.fromFilePairs("$projectDir/tests/input/pipeline/example.{bim,bed,fam}", size: 3)
+                     input[1] = file("$projectDir/tests/input/pipeline/phenotype.txt")
                     """
                 }
             }
@@ Expand Down @@