Set chunk prepare channel as function

nf-core · Mar 3, 2025 · f8e7eff · f8e7eff
1 parent 9368068
commit f8e7eff
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Showing 6 changed files with 67 additions and 164 deletions.
diff --git a/subworkflows/local/chunk_prepare_channel/tests/main.nf.test.snap b/subworkflows/local/chunk_prepare_channel/tests/main.nf.test.snap
diff --git a/subworkflows/local/chunk_prepare_channel/tests/tags.yml b/subworkflows/local/chunk_prepare_channel/tests/tags.yml
diff --git a/...flows/local/chunk_prepare_channel/main.nf → workflows/phaseimpute/function.nf b/...flows/local/chunk_prepare_channel/main.nf → workflows/phaseimpute/function.nf
@@ -1,11 +1,4 @@
-workflow CHUNK_PREPARE_CHANNEL {
-
-    take:
-    ch_chunks // channel:   [ [id, chr], txt ]
-    tool
-
-    main:
-
+def chunkPrepareChannel(ch_chunks, tool) {
     if(tool == "glimpse"){
         ch_chunks = ch_chunks.map { chr, txt -> [chr, file(txt)]}
                 .splitCsv(header: ['ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'], sep: "\t", skip: 0)
@@ -20,8 +13,5 @@ workflow CHUNK_PREPARE_CHANNEL {
     } else {
         error "Only 'glimpse' and 'quilt' output format are supported. Got ${tool}"
     }
-
-    emit:
-    chunks  = ch_chunks // channel:   [ [meta], regionstart, regionend ]
-
+    return ch_chunks // channel:   [ [meta], regionstart, regionend ]
 }
diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
@@ -32,9 +32,9 @@ include { GAWK as FILTER_CHR_DWN                     } from '../../modules/nf-co
 include { VCF_NORMALIZE_BCFTOOLS                     } from '../../subworkflows/local/vcf_normalize_bcftools'
 include { VCF_SITES_EXTRACT_BCFTOOLS                 } from '../../subworkflows/local/vcf_sites_extract_bcftools'
 include { VCF_PHASE_SHAPEIT5                         } from '../../subworkflows/local/vcf_phase_shapeit5'
-include { CHUNK_PREPARE_CHANNEL                      } from '../../subworkflows/local/chunk_prepare_channel'
 include { VCF_CONCATENATE_BCFTOOLS as CONCAT_PANEL   } from '../../subworkflows/local/vcf_concatenate_bcftools'
 include { BCFTOOLS_STATS as BCFTOOLS_STATS_PANEL     } from '../../modules/nf-core/bcftools/stats'
+include { chunkPrepareChannel                        } from './function.nf'
 
 // Imputation
 include { LISTTOFILE                                 } from '../../modules/local/listtofile'
@@ -291,8 +291,7 @@ workflow PHASEIMPUTE {
 
             // Use chunks from parameters if provided or use previous chunks from panelprep
             if (params.chunks) {
-                CHUNK_PREPARE_CHANNEL(ch_chunks, "glimpse")
-                ch_chunks_glimpse1 = CHUNK_PREPARE_CHANNEL.out.chunks
+                ch_chunks_glimpse1 = chunkPrepareChannel(ch_chunks, "glimpse")
             }
 
             // Glimpse1 subworkflow
@@ -330,8 +329,7 @@ workflow PHASEIMPUTE {
             log.info("Impute with GLIMPSE2")
 
             if (params.chunks) {
-                CHUNK_PREPARE_CHANNEL(ch_chunks, "glimpse")
-                ch_chunks_glimpse2 = CHUNK_PREPARE_CHANNEL.out.chunks
+                ch_chunks_glimpse2 = chunkPrepareChannel(ch_chunks, "glimpse")
             }
 
             // Run imputation
@@ -378,8 +376,7 @@ workflow PHASEIMPUTE {
 
             // Use provided chunks if --chunks
             if (params.chunks) {
-                CHUNK_PREPARE_CHANNEL(ch_chunks, "quilt")
-                ch_chunks_quilt = CHUNK_PREPARE_CHANNEL.out.chunks
+                ch_chunks_quilt = chunkPrepareChannel(ch_chunks, "quilt")
             }
 
             // Impute BAMs with QUILT

diff --git a/.../chunk_prepare_channel/tests/main.nf.test → workflows/phaseimpute/tests/function.nf.test b/.../chunk_prepare_channel/tests/main.nf.test → workflows/phaseimpute/tests/function.nf.test
@@ -1,22 +1,18 @@
-nextflow_workflow {
+nextflow_function {
+    /*
+    The following tests are for the functions in the main.nf script
+    They are tested using the --verbose argument
+    */
 
-    name "Test Subworkflow CHUNK_PREPARE_CHANNEL"
-    script "../main.nf"
-
-    workflow "CHUNK_PREPARE_CHANNEL"
-
-    tag "subworkflows"
-    tag "subworkflows_local"
-    tag "subworkflows/chunk_prepare_channel"
-    tag "chunk_prepare_channel"
+    name "Test function phaseimpute"
+    script "../function.nf"
+    tag "function"
 
     test("Prepare chunks channel Glimpse") {
+        function "chunkPrepareChannel"
+        tag "chunkPrepareChannel"
         when {
-            params {
-                max_cpus   = 2
-                max_memory = '2.GB'
-            }
-            workflow {
+            function {
                 """
                 input[0] = Channel.of([
                     [id: "1000GP", chr: "chr21"],
@@ -29,19 +25,16 @@ nextflow_workflow {
 
         then {
             assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() },
+                { assert function.success }
             )
         }
     }
 
     test("Prepare chunks channel Quilt") {
+        function "chunkPrepareChannel"
+        tag "chunkPrepareChannel"
         when {
-            params {
-                max_cpus   = 2
-                max_memory = '2.GB'
-            }
-            workflow {
+            function {
                 """
                 input[0] = Channel.of([
                     [id: "1000GP", chr: "chr21"],
@@ -54,19 +47,16 @@ nextflow_workflow {
 
         then {
             assertAll(
-                { assert workflow.success },
-                { assert snapshot(workflow.out).match() },
+                { assert function.success }
             )
         }
     }
 
     test("Prepare chunks channel error tool") {
+        function "chunkPrepareChannel"
+        tag "chunkPrepareChannel"
         when {
-            params {
-                max_cpus   = 2
-                max_memory = '2.GB'
-            }
-            workflow {
+            function {
                 """
                 input[0] = Channel.of([
                     [id: "1000GP", chr: "chr21"],
@@ -79,8 +69,8 @@ nextflow_workflow {
 
         then {
             assertAll(
-                { assert workflow.failed },
-                { assert snapshot(workflow.stdout).match() }
+                { assert function.failed },
+                { assert function.stdout.contains("Only 'glimpse' and 'quilt' output format are supported. Got glimpse2") }
             )
         }
     }

diff --git a/workflows/phaseimpute/tests/function.nf.test.snap b/workflows/phaseimpute/tests/function.nf.test.snap
@@ -0,0 +1,40 @@
+{
+    "Prepare chunks channel Quilt": {
+        "content": [
+            {
+
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-03-03T16:53:24.615848886"
+    },
+    "Prepare chunks channel error tool": {
+        "content": [
+            [
+                "N E X T F L O W  ~  version 24.10.4",
+                "Launching `/home/llenezet/repositories/phaseimpute/.nf-test-dd0d5421ca2fe0df9ae90be137523768.nf` [scruffy_fermat] DSL2 - revision: d78e86493b",
+                "Only 'glimpse' and 'quilt' output format are supported. Got glimpse2"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-03-03T16:59:53.809041216"
+    },
+    "Prepare chunks channel Glimpse": {
+        "content": [
+            {
+
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-03-03T16:53:17.567651555"
+    }
+}