Added nf-test for gstama/polyacleanup (#6299)

Co-authored-by: Simon Pearce <[email protected]>
nf-core · Aug 26, 2024 · 8684e27 · 8684e27
1 parent e98430a
commit 8684e27
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Showing 7 changed files with 78 additions and 38 deletions.
diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test
@@ -0,0 +1,42 @@
+
+nextflow_process {
+
+    name "Test Process GSTAMA_POLYACLEANUP"
+    script "../main.nf"
+    process "GSTAMA_POLYACLEANUP"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gstama"
+    tag "gstama/polyacleanup"
+
+    test("test-gstama-polyacleanup") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/transcriptome.fasta', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.report[0][1]).linesGzip[0..2],
+					path(process.out.fasta[0][1]).linesGzip[3..7],
+					path(process.out.tails[0][1]).linesGzip[3..7],
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap b/modules/nf-core/gstama/polyacleanup/tests/main.nf.test.snap
@@ -0,0 +1,33 @@
+{
+    "test-gstama-polyacleanup": {
+        "content": [
+            [
+                "polya_num\tpolya_num_count",
+                "0\t11",
+                "1\t1"
+            ],
+            [
+                "GGAAGCACTTTTTTCCTGTATAGCAAAATGAGTTCAAGATATTCTTTGCCTAATTTCAGCTCTAGCTAGAACCAGTCAATATGGAAATAAACAATGAGGGTATCTAACCTACTGAACACTGAACCATCAGCCTAACTCTATGCAATATAGTCATACTAAAATATTTCTCATAAAAAAGTTCTTAACAGTTCGTTCACTATATCTTTCACGCAGTTATTTTATAGAATAAGCAAAGTAGGGCATGTGAAACACTTTAGCTTAGCTTCTAGCATCCAGTAGCGGTGCTCAAAAATGTTAGATCATTTATGTAACAATCTGCTAGGTTATAACATTCAGTGAGCCTTGGTACTTTTCATTGAACAGCTGGTATAGAGGCTAGGGATAGGGAGCTGCAGTTCATTTTCCATGCCCCTACCCGAGTTCTCTTGGCTAAATGTGATACGCATTTAAGGCCCAGAACCTGCTGTTTAAAAGGTTGTGGTAAACTATTTTGTATACCAAAGACTTCTCTGTAATAAAGTATGTAAGTACACATGAACATTTTATATGCACGCACATTTTAAATCATCTGCACATTGAGATTCTACACTTTTCTCAAGGGCACATCTCTATTCCGTTTCTTTGTAAATTTGACTTCTACCTAACAATATGCAATTGCTGGGATTTTTTTCCCTAACAGTATGAAAGTTGTCTTTAAATAGTAAAAGCACCACAATCTATTAACACCACATGTTATCTTTAAACTGAAATATTTTAGTGATGTCTTGGACATCAAAATAATTTCTTAAGGTGGACTCTTGAGTATGTGGGTCCAGCCCAGGTCTGCAGTTTGTGCAGACATAGAAAAAAGAGGAACTTTAAATATTCAGAAAAAGTTAACAGGCTAGCTTTAAAATACTGCTGGAAATTAAATTTCTTCAGAGTTGGCAAGCATGGGCTATTGATCAAAATATGAATTAAACGGATTTACATCATTAAGAAAAAAACAAATCCATGTTATTGTGCTGTGAAATTTCCATGATGCCTTTCAAATAGGCTGCTCACAAATTTTTTTATAATTCTAAATCACTCGCTTTTTGATGGAAAAAAGAATACAGATGGACTGTGTTTTACCTATGTGAAAGTCACCAATCCATTTAAAATAAAATCCAAGAGGGCATATACAGTCTAATCAAGTCATCATTTTCCTGATTAATAAGAACTACACTTTACACAAAATACTTTATCAGCAGCTGTTTTCATCAAAAAATCAGTAGTCAGTTTCACAGTTGAAAAAGTTACACATTAAAATATTTTACAATTCATTATATATTCACCAGGTTCCCATTTTCTAAGGGGCTTTTAATATAAAGCAGAATAGAACACTGTCTCTACTAAAAATACAAAAATTAGCTGGGAGTGGTGGCATGCTCCTATAGTCCTAGCTACTCAGGAGGCTGAGGTGGGAGGATGGCTTGAACCCAGGAGGTCAAGGCTGCAGTGAGCCGAAATTGCACCACTGCATTCCAGGCCGGGCAAAAGAGCCAGACCCTGTCTCAAAAAAAAAAGTTTACATTGTATTTCCTACTCTTAGTTACACTAAGCTAGACAGCAGATGACTAGAGGGTGTGATATATTTACTGAGTGACTCGAAATCCATTTTAAACTTGGAAATGTAAAAACTAACTTCTTTCCACTCATTTTCAGGGTCATTACTGAGAGATAATAAATGACAGAATAAGGAAATAATCACTGTAAATACTTAGGGACCTGAATAAGAGAAAGGAAGGGAAAGTAAAGGGATCTAACATTTATTGGGCACCTTCTGTGTTCCAAGGATTGTGATAGGTTCTTTGCATATCTCATGTAATTTAATTCTCACAATGGCCTTACGAAGCAGGTATTATTCCCATTTTACAGACAAAGAAAATGAGTCTTGAGAGCCTGCATAACGTGTCTAACACTACACAGATGAGAGGCAGTGGAACTTGGTTCCAAATCCTAATCTGCTTGATTCCAAGGACCATGATCTGTATATACACTGGGCTTCTAAACAACTCTGCCCCACTGCAGTGAAAAGAGTCTCAAACACAGACTAGAGTCACACAACTTTTGTGTTTCATCCTTCTTCTCCTGTTTGACAATGTCAGTTAAGTTAATGAGCTTTTCCATTGCCTCGACTTGCCTATTCAGGTGCTTCAAATACATCCCACATGCACGACAATAGGACTCCAAAAGCAGGCCAAACCTCTGGCTAAGTGTTTTATTGTGCATCTCAGATCTAAAAGAATCATGCAAAATTAGAAAAATATATATATAGTCTTAAATCAGTATACAAATAATCTTTGCTAAACAATTTAAACACTCATTTTTGAAATCCAATAAATGTTACAATCATACTAATAATAACATTATTCAAAACCTGTAATTTAGAAGCAAAACCACCATGAGTTTCAGGTAGTTCCTGAATATGTGATTAAATAAACATCTAGTTTTTAGGTTTATTTCAACTAGTTTTCATTGACTAATCTCAGTACAAGATATAAAAGCATGAAAAAAGGAAATTGAGCACAAAAATAATCAAATGAAGAGGGAGGGAACAAAGCGCTCAGTGAATGCTGTTTGACTCTTCTGACACACGTCTACGCTTCTTGTTTTCAACTTAACTTCTGGGTTCCATTTTTAAATTTTAACACTTAAAATATCATATTAGATATAAATCTGTTTCTAAATTTATGAAAAGTTATATGGTTTATGACCTGTAACTTTTGAGTACTGCATATATCACATTCTACAAAACATTTTTTATTCTTAATTAGCTTGTTTTTCAGTAAGAACCACGGGAGTTTGACATTATTGTTCTGAATCTCAAGGTAAAACATTTTTTTTCTTTTTTTGGGGATATTTTAATCCATACACACAGTGAAACCTACAGCAATATTCATCTGGACCTAGAAAATTTTACTTAAGTAGAACAAAAATCTTTAAAAATATTTAAGCTCTCATTCATGACTGAAATTTAGTTTTGAATTTATTACTTTTTAAATTTCAAAGAGCAAAAGTTGAGAAGCTCATCACTGGTACAAAATAGTTTTAGTATGGAAAACTCTTCCAGCCAAACATAAACAAAAGTATATAAGTAATACATATTTATAAATCTATTAAGAAAGCAAGTAATATGTACCTTAAGAATTTAATGGGAAAATAATTAGACTTACTTTAAATGCCAAAAGAAAAAGTGCCCAATCCTTTGATTAGTCAATGCTTTCTTCAGTAAAAATCTCACAAGCAAGTTATCCAAATATTGTTCATATTTTAGGACCTAGGTGATTCAAAAAAAACAAATCAGGTTCAGTTTCTGCATGGCCGATCTAAAGAAAATTTTTTCAGAAAGAAAGTGGATATTACTG",
+                ">ENST00000472972",
+                "AACCTACTGAACACTGAACCATCAGCCTAACTCTATGCAATATAGTCATACTAAAATATTTCTCATAAAAAAGTTCTTAACAGTTCGTTCACTATATCTTTCACGCAGTTATTTTATAGAATAAGCAAAGTAGGGCATGTGAAACACTTTAGCTTAGCTTCTAGCATCCAGTAGCGGTGCTCAAAAATGTTAGATCATTTATGTAACAATCTGCTAGGTTATAACATTCAGTGAGCCTTGGTACTTTTCATTGAACAGCTGGTATAGAGGCTAGGGATAGGGAGCTGCAGTTCATTTTCCATGCCCC",
+                ">ENST00000359963 CDS=261-1934",
+                "TTTCTTTAAATAAAAACATGAAGGAACATAAAATTTCTTTTCATGCGCTTAGTTCCTTTCCAGTTCTCGACTTTTTTTGTTTTTTTTTTTTGAGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGTGTGCAGTGGCGTGATCTTGGCTCACTGCAACCTCCGCCTCCCAGGTTCAAGCGATTTTCCTGCCTCAGCCTCCTGAATAGCTGGGACTACAGGTGCGCGCCACCACGCCCAGCTATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATATTGACCAGGCTGGTCTCGAACTCCTGACCTCATGATCCTCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCGAGAGCCACTGTGCCCAGCCAGTTCTTGACCTTTTCATTTTGTGTTTCTATCAGATGCTCTTCCTTTCCTATGATAAGAGCAGGATTCAATTCTATTAAGATTTTTAAACTGAGTACCTATGTGGGCTTTGGGCGTGCAAAACACAGTGCAGCAATCTCTTCCCAACTATTTGAGCATTCCCTGCATGATATTCTGACATATATGGACTTATGTCTAGATGTCACTTTAGGAGTCTGAAAACATCAGTTGCAGCTTACAAGAGTGGTCAGTCCTTCCTGTTGTGGTTATTTGAAAAAAAAGAAGGGACTATCATCTTAAAGCACAGAGAGAGAGAGAGAGCAGGAGAAAGAGCTGCTGTGGTGGCAGGCAGAAATGTAACTTAAAAAGAAAAAAATCCTTGCCTGGCAAAGTGGCTCATGCCTATAATTCCTGCACTTTGGGAGGCTGAGACAGGAAGATCGCTTGAGTCCAGGAGTTCAAGACTAGCCTGGACAACATAGTGAGACCCTATCTCTACAAAAATAAAAATTAAAAAAAATTAGCCAGGCATGGGCCGGGCATGGTGGCTCAAGCCTTTAATCCCAGCACTTTGGGAGCCCAAGGTGGGTGGATCAGCTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACGTGGAGAAACCCCATCTCTACTAAAAATACAAAACAGTAGCCGGATGTGATGGCACATGCCTGTAATCCCAGCTATTTGAGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCAGAGGTTGTGGTGAGCTGAGATGACACTATTGTACCCCAGCCTGGGCAACAAGAGCAAAACTCTGCCTCAAAAAAAAAAAAAAAAAAAAAAATTAGCCAGGCGTGGTGATGCATACCTGTAGTCCCAGCTACTCAGGAGGCTGAGTGGGGGGATCACTTAAGCCCAGGAGATCGAGGTTGCAGTGAGCTGTGATTGTGCCACTGCACTCCAGCCTAAGAGACAGAGCAAGACCCTGTCTCAACAAAACAAAACAAAACCAGCAAACATCCTTGGCATAGATAACAGAAGATAAGAACACATACTTTAGGACTATACTAAGGTTGCTGTGTAGGTGAGGAGAAAGCTGAGGGTAGGGGGAAGGGCTAGGATTGGACAACCTTGGGCATTAAAGAAGGGGTTTGAGCAGAGCTGAGTGGGTTTGGCACCTAATACGCAAAGCTTTTTCCACTTTTTTAACTTCCAAGTTACTCTAGGAAAAATCAGAACCTATGGGACAGAATCTAGGAGATGAGAAGGTACAATCTTTTAGAATCATAAAAATAAAAAAGCTTTAGGCATATGCAGAGAGAATGAGACTCAAGAAACCATTGTCTTATAGCACGCATATTAGCCGCAACACAGCAAAACAAAATTTTATTTATTTATTTATTTATTTTGAGACAGAGTCTTGCTCTGTCACCCAGGCATAGTGACTGGTGTGGCCCAGGCACCAGTGCAGCAGTGCAGTCTCAGCTCACTGCAACCTCTGCCTCCTGGGCTCAAATGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTCCACCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCGCCATGTTGGTCAGGGTGGTCTCAAACTTTGGACCTCAGGTGATCCACCTGCCTCGGCCTCCCCAAATGCTGAGATTACAG"
+            ],
+            [
+                "",
+                ">tail_ENST00000472972",
+                "",
+                ">tail_ENST00000359963 CDS=261-1934",
+                ""
+            ],
+            [
+                "versions.yml:md5,dff6214a93a250748705dbd8ec455fec"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T10:44:18.309783"
+    }
+}
diff --git a/modules/nf-core/gstama/polyacleanup/tests/nextflow.config b/modules/nf-core/gstama/polyacleanup/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.prefix = { "${meta.id}_tama" }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -524,9 +524,6 @@ gsea/gsea:
 gstama/collapse:
   - modules/nf-core/gstama/collapse/**
   - tests/modules/nf-core/gstama/collapse/**
-gstama/polyacleanup:
-  - modules/nf-core/gstama/polyacleanup/**
-  - tests/modules/nf-core/gstama/polyacleanup/**
 gubbins:
   - modules/nf-core/gubbins/**
   - tests/modules/nf-core/gubbins/**

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