Glimpse2 splitreference: Change python test to nf-test (nf-core#5076)

* Glimpse2 splitreference: Change python test to nf-test * Update modules/nf-core/glimpse2/splitreference/tests/main.nf.test Co-authored-by: Maxime U Garcia <[email protected]> * Update modules/nf-core/glimpse2/splitreference/tests/main.nf.test Co-authored-by: Maxime U Garcia <[email protected]> * Update modules/nf-core/glimpse2/splitreference/tests/main.nf.test Co-authored-by: Maxime U Garcia <[email protected]> * Update main.nf.test * Update modules/nf-core/glimpse2/splitreference/tests/nextflow.config Co-authored-by: Maxime U Garcia <[email protected]> * Update modules/nf-core/glimpse2/splitreference/tests/main.nf.test Co-authored-by: Maxime U Garcia <[email protected]> * Update modules/nf-core/glimpse2/splitreference/tests/main.nf.test Co-authored-by: Maxime U Garcia <[email protected]> * Update modules/nf-core/glimpse2/splitreference/meta.yml Co-authored-by: Matthias Hörtenhuber <[email protected]> * Update snapshot with version file --------- Co-authored-by: LouisLeNezet <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]> Co-authored-by: Matthias Hörtenhuber <[email protected]>
LouisLeNezet · Mar 13, 2024 · fa12139 · fa12139
1 parent 5154596
commit fa12139
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Showing 8 changed files with 97 additions and 49 deletions.
diff --git a/modules/nf-core/glimpse2/splitreference/meta.yml b/modules/nf-core/glimpse2/splitreference/meta.yml
@@ -4,14 +4,15 @@ keywords:
   - split
   - reference
   - phasing
+  - imputation
 tools:
   - "glimpse2":
       description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies."
       homepage: "https://odelaneau.github.io/GLIMPSE"
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 requirements:
   - AVX2
 input:
@@ -36,6 +37,11 @@ input:
       type: string
       description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
       pattern: "chrXX:leftBufferPosition-rightBufferPosition"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing genomic map information
+        e.g. `[ map:'GRCh38' ]`
   - map:
       type: file
       description: File containing the genetic map.

diff --git a/modules/nf-core/glimpse2/splitreference/tests/main.nf.test b/modules/nf-core/glimpse2/splitreference/tests/main.nf.test
@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process GLIMPSE2_SPLITREFERENCE"
+    script "../main.nf"
+    config "./nextflow.config"
+
+    process "GLIMPSE2_SPLITREFERENCE"
+
+    tag "modules_nfcore"
+    tag "modules"
+    tag "glimpse2"
+    tag "glimpse2/splitreference"
+
+    test("Should run without map") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'ref1000GP', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true),
+                    "chr21:16600000-16800000",
+                    "chr21:16600000-16800000"
+                ]
+                input[1]= [[ id:'map'],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                // File has a timestamp in it and is in binary format, so we can only check the name
+                { assert file(process.out.bin_ref[0][1]).name == "ref1000GP_chr21_16600000_16800000.bin" },
+                { assert snapshot(process.out.version).match()}
+            )
+        }
+
+    }
+
+    test("Should run with map") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'ref1000GP', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true),
+                    "chr21:16600000-16800000",
+                    "chr21:16600000-16800000"
+                ]
+                input[1]= [[ id:'map'], file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                // File has a timestamp in it and is in binary format, so we can only check the name
+                { assert file(process.out.bin_ref[0][1]).name == "ref1000GP_chr21_16600000_16800000.bin" },
+                { assert snapshot(process.out.version).match()}
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/glimpse2/splitreference/tests/main.nf.test.snap b/modules/nf-core/glimpse2/splitreference/tests/main.nf.test.snap
diff --git a/...e/glimpse2/splitreference/nextflow.config → ...pse2/splitreference/tests/nextflow.config b/...e/glimpse2/splitreference/nextflow.config → ...pse2/splitreference/tests/nextflow.config
@@ -6,6 +6,4 @@ process {
         ].join(' ')
         ext.prefix = { "${meta.id}" }
     }
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
 }
diff --git a/modules/nf-core/glimpse2/splitreference/tests/tags.yml b/modules/nf-core/glimpse2/splitreference/tests/tags.yml
@@ -0,0 +1,2 @@
+glimpse2/splitreference:
+  - modules/nf-core/glimpse2/splitreference/**
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -914,9 +914,6 @@ glimpse2/concordance:
 glimpse2/ligate:
   - modules/nf-core/glimpse2/ligate/**
   - tests/modules/nf-core/glimpse2/ligate/**
-glimpse2/splitreference:
-  - modules/nf-core/glimpse2/splitreference/**
-  - tests/modules/nf-core/glimpse2/splitreference/**
 glnexus:
   - modules/nf-core/glnexus/**
   - tests/modules/nf-core/glnexus/**

diff --git a/tests/modules/nf-core/glimpse2/splitreference/main.nf b/tests/modules/nf-core/glimpse2/splitreference/main.nf
diff --git a/tests/modules/nf-core/glimpse2/splitreference/test.yml b/tests/modules/nf-core/glimpse2/splitreference/test.yml
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		glimpse2/splitreference:
		- modules/nf-core/glimpse2/splitreference/**