tests: switch bivariateremlldms setup to makegrmpart

Author: lyh970817

modules/nf-core/gcta/bivariateremlldms/tests/helpers/makegrm/main.nf

@@ -7,7 +7,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "gcta"
     tag "gcta/bivariateremlldms"
-    tag "tests/helpers/makegrm"
+    tag "gcta/makegrmpart"
     tag "gawk"
 
     setup {
@@ -73,15 +73,24 @@ nextflow_process {
             }
         }
 
-        run("GCTA_MAKEGRM_HELPER", alias: "GCTA_MAKEGRM_LDMS1") {
-            script "../tests/helpers/makegrm/main.nf"
+        run("GCTA_MAKEGRMPART", alias: "GCTA_MAKEGRM_LDMS1") {
+            script "../../makegrmpart/main.nf"
             process {
                 """
+                file('plink_simulated.mbfile').text = 'plink_simulated\\n'
+
                 input[0] = [
-                    [ id:'plink_simulated_ldms1.part_1_1' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                    [ id:'plink_simulated_ldms1', part_gcta_job:1, nparts_gcta:1 ],
+                    file('plink_simulated.mbfile'),
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                    ]
                 ]
                 input[1] = [
                     [ id:'plink_random_selected_snp' ],
@@ -91,15 +100,24 @@ nextflow_process {
             }
         }
 
-        run("GCTA_MAKEGRM_HELPER", alias: "GCTA_MAKEGRM_LDMS2") {
-            script "../tests/helpers/makegrm/main.nf"
+        run("GCTA_MAKEGRMPART", alias: "GCTA_MAKEGRM_LDMS2") {
+            script "../../makegrmpart/main.nf"
             process {
                 """
+                file('plink_simulated.mbfile').text = 'plink_simulated\\n'
+
                 input[0] = [
-                    [ id:'plink_simulated_ldms2.part_1_1' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                    [ id:'plink_simulated_ldms2', part_gcta_job:1, nparts_gcta:1 ],
+                    file('plink_simulated.mbfile'),
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bed', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bim', checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.fam', checkIfExists: true)
+                    ]
                 ]
                 input[1] = GAWK_COMPLEMENT_VARIANTS.out.output
                 """