Added nf-test for angsd/contamination (#6602)

* Added nf-test for angsd/contamination * Swap container version * Update snapshot --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: Phil Ewels <[email protected]>
nf-core · Sep 9, 2024 · 97504fc · 97504fc
1 parent 9897e69
commit 97504fc
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Showing 9 changed files with 162 additions and 48 deletions.
diff --git a/modules/nf-core/angsd/contamination/main.nf b/modules/nf-core/angsd/contamination/main.nf
@@ -4,8 +4,8 @@ process ANGSD_CONTAMINATION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0':
-        'biocontainers/angsd:0.939--h468462d_0' }"
+        'https://depot.galaxyproject.org/singularity/angsd:0.940--hf5e1c6e_3':
+        'biocontainers/angsd:0.940--hf5e1c6e_3' }"
 
     input:
     tuple val(meta), path(icounts)
@@ -30,6 +30,18 @@ process ANGSD_CONTAMINATION {
         2> >(tee ${prefix}.txt >&2)
 
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        angsd: \$(echo \$(angsd 2>&1) | grep version | head -n 1 | sed 's/.*version: //g;s/ .*//g')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         angsd: \$(echo \$(angsd 2>&1) | grep version | head -n 1 | sed 's/.*version: //g;s/ .*//g')

diff --git a/modules/nf-core/angsd/contamination/meta.yml b/modules/nf-core/angsd/contamination/meta.yml
@@ -22,6 +22,11 @@ input:
       type: file
       description: Internal format for dumping binary single chrs. Useful for ANGSD contamination
       pattern: "*.icnts.gz"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing information related to the hapmap_file.
+        e.g. [ id:'test' ]
   - hapmap_file:
       type: file
       description: A list of variable sites to look for heterozygosity.

diff --git a/modules/nf-core/angsd/contamination/tests/main.nf.test b/modules/nf-core/angsd/contamination/tests/main.nf.test
@@ -0,0 +1,78 @@
+
+nextflow_process {
+
+    name "Test Process ANGSD_CONTAMINATION"
+    script "../main.nf"
+    process "ANGSD_CONTAMINATION"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "angsd"
+    tag "angsd/contamination"
+    tag "angsd/docounts"
+
+    setup {
+        run("ANGSD_DOCOUNTS") {
+            script "../../../angsd/docounts/main.nf"
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true),
+				    []
+				]
+
+                """
+            }
+        }
+    }
+
+    test("test-angsd-contamination") {
+
+        when {
+            process {
+                """
+                input[0] = ANGSD_DOCOUNTS.out.icounts
+				input[1] = [ [id:'test2'], file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/angsd/HapMapChrX.gz")]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					file(process.out.txt[0][1]).readLines()[3..7],
+                    file(process.out.versions[0]).readLines(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-angsd-contamination-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = ANGSD_DOCOUNTS.out.icounts
+				input[1] = [ [id:'test2'], file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/angsd/HapMapChrX.gz")]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/angsd/contamination/tests/main.nf.test.snap b/modules/nf-core/angsd/contamination/tests/main.nf.test.snap
@@ -0,0 +1,60 @@
+{
+    "test-angsd-contamination": {
+        "content": [
+            [
+                "Seed value of 0 (zero) will use time as seed",
+                "-----------------",
+                "[readhap] We now have: 58190 snpSites after filtering based on hapMapfile",
+                "[readicnts] fname:test.icnts.gz minDepth:2 maxDepth:200",
+                "[readicnts] Has read:1557012 sites,  1517472 sites (after depfilter) from ANGSD icnts file"
+            ],
+            [
+                "\"ANGSD_CONTAMINATION\":",
+                "    angsd: 0.940-dirty"
+            ],
+            [
+                "versions.yml:md5,e496b7eb11be581adf1781883ba2abff"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-09T05:53:42.620175303"
+    },
+    "test-angsd-contamination-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,e496b7eb11be581adf1781883ba2abff"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e496b7eb11be581adf1781883ba2abff"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-09T05:53:56.844309422"
+    }
+}
diff --git a/modules/nf-core/angsd/contamination/tests/nextflow.config b/modules/nf-core/angsd/contamination/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: ANGSD_DOCOUNTS {
+        ext.args = "-iCounts 1 -doDepth -dumpCounts 2"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1,9 +1,6 @@
 amps:
   - modules/nf-core/amps/**
   - tests/modules/nf-core/amps/**
-angsd/contamination:
-  - modules/nf-core/angsd/contamination/**
-  - tests/modules/nf-core/angsd/contamination/**
 arriba/arriba:
   - modules/nf-core/arriba/arriba/**
   - tests/modules/nf-core/arriba/arriba/**

diff --git a/tests/modules/nf-core/angsd/contamination/main.nf b/tests/modules/nf-core/angsd/contamination/main.nf
diff --git a/tests/modules/nf-core/angsd/contamination/nextflow.config b/tests/modules/nf-core/angsd/contamination/nextflow.config
diff --git a/tests/modules/nf-core/angsd/contamination/test.yml b/tests/modules/nf-core/angsd/contamination/test.yml