add-UTILS-groovy-lib-update-snapshots

nf-core · Jun 20, 2023 · 9f357aa · 9f357aa
1 parent d16c2da
commit 9f357aa
Show file tree

Hide file tree

Showing 20 changed files with 101 additions and 461 deletions.
diff --git a/nf-test.config b/nf-test.config
@@ -1,8 +1,16 @@
 config {
-
+    // location for all nf-tests
     testsDir "tests"
+
+    // nf-test directory including temporary files for each test
     workDir ".nf-test"
+
+    // location of library folder that is added automatically to the classpath
+    libDir "tests/pipeline/lib/"
+
+    // location of an optional nextflow.config file specific for executing tests
     configFile "nextflow.config"
-    profile ""
 
+    // run all test with the defined docker profile from the main nextflow.config
+    profile ""
 }
diff --git a/tests/pipeline/lib/UTILS.groovy b/tests/pipeline/lib/UTILS.groovy
@@ -0,0 +1,11 @@
+// Function to remove Nextflow version from software_versions.yml
+
+class UTILS {
+    public static String removeNextflowVersion(outputDir) {
+        def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
+        if (softwareVersions.containsKey("Workflow")) {
+            softwareVersions.Workflow.remove("Nextflow")
+        }
+        return softwareVersions
+    }
+}
diff --git a/tests/pipeline/misc/custom_reftax.nf.test b/tests/pipeline/misc/custom_reftax.nf.test
@@ -14,13 +14,9 @@ nextflow_pipeline {
         }
 
         then {
-            // Remove Nextflow version from software_versions.yml
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/overall_summary.tsv")).match("overall_summary_tsv") },
                 { assert snapshot(path("$outputDir/barrnap/rrna.arc.gff"),
                                 path("$outputDir/barrnap/rrna.bac.gff"),

diff --git a/tests/pipeline/misc/custom_reftax.nf.test.snap b/tests/pipeline/misc/custom_reftax.nf.test.snap
@@ -3,66 +3,25 @@
         "content": [
             "Samplesheet.tsv:md5,dbf8d1a2b7933dab9e5a139f33c2b1f4"
         ],
-        "timestamp": "2023-05-25T21:00:42+0000"
+        "timestamp": "2023-05-28T21:18:54+0000"
     },
     "cutadapt": {
         "content": [
             "cutadapt_summary.tsv:md5,5d02749984a811479e7d534fda75163f"
         ],
-        "timestamp": "2023-05-25T21:00:42+0000"
+        "timestamp": "2023-05-28T21:18:54+0000"
     },
     "software_versions": {
         "content": [
-            {
-                "BARRNAP": {
-                    "barrnap": "0.9"
-                },
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUTADAPT_BASIC": {
-                    "cutadapt": "3.4"
-                },
-                "DADA2_DENOISING": {
-                    "R": "4.1.1",
-                    "dada2": "1.22.0"
-                },
-                "DADA2_FILTNTRIM": {
-                    "R": "4.1.1",
-                    "dada2": "1.22.0"
-                },
-                "DADA2_QUALITY1": {
-                    "R": "4.1.1",
-                    "ShortRead": "1.52.0",
-                    "dada2": "1.22.0"
-                },
-                "DADA2_TAXONOMY": {
-                    "R": "4.1.1",
-                    "dada2": "1.22.0"
-                },
-                "FASTQC": {
-                    "fastqc": "0.11.9"
-                },
-                "RENAME_RAW_DATA_FILES": {
-                    "sed": "4.7"
-                },
-                "TRUNCLEN": {
-                    "pandas": "1.1.5",
-                    "python": "3.9.1"
-                },
-                "Workflow": {
-                    "nf-core/ampliseq": "2.6.0dev"
-                }
-            }
+            "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, FASTQC={fastqc=0.11.9}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.6.0dev}}"
         ],
-        "timestamp": "2023-05-25T21:00:42+0000"
+        "timestamp": "2023-05-28T21:18:54+0000"
     },
     "overall_summary_tsv": {
         "content": [
             "overall_summary.tsv:md5,3231d6ee72b9a1e7742e5605caaff05a"
         ],
-        "timestamp": "2023-05-25T21:00:42+0000"
+        "timestamp": "2023-05-28T21:18:54+0000"
     },
     "dada2": {
         "content": [
@@ -72,7 +31,7 @@
             "DADA2_table.rds:md5,d095501019ce7ebccfa0eb801db1ed29",
             "DADA2_table.tsv:md5,5c9fb0bfd70da165f0ce6a361bfe0b43"
         ],
-        "timestamp": "2023-05-25T21:00:42+0000"
+        "timestamp": "2023-05-28T21:18:54+0000"
     },
     "barrnap": {
         "content": [
@@ -81,14 +40,14 @@
             "rrna.euk.gff:md5,c9bc1d9d8fb77dc19c95dee2d53840eb",
             "rrna.mito.gff:md5,df19e1b84ba6f691d20c72b397c88abf"
         ],
-        "timestamp": "2023-05-25T21:00:42+0000"
+        "timestamp": "2023-05-28T21:18:54+0000"
     },
     "multiqc": {
         "content": [
             "multiqc_fastqc.txt:md5,3a4417c7d95a9bbe17751dc974157cd3",
             "multiqc_general_stats.txt:md5,88c2b9e6d02b83afe4f9551e6c9a91a7",
             "multiqc_cutadapt.txt:md5,330a7b72dc671ca99fcb3fb84b6776c1"
         ],
-        "timestamp": "2023-05-25T21:00:42+0000"
+        "timestamp": "2023-05-28T21:18:54+0000"
     }
 }
diff --git a/tests/pipeline/misc/doubleprimers.nf.test b/tests/pipeline/misc/doubleprimers.nf.test
@@ -14,13 +14,9 @@ nextflow_pipeline {
         }
 
         then {
-            // Remove Nextflow version from software_versions.yml
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/overall_summary.tsv")).match("overall_summary_tsv") },
                 { assert snapshot(path("$outputDir/barrnap/rrna.arc.gff"),
                                 path("$outputDir/barrnap/rrna.bac.gff"),

diff --git a/tests/pipeline/misc/doubleprimers.nf.test.snap b/tests/pipeline/misc/doubleprimers.nf.test.snap
@@ -3,62 +3,25 @@
         "content": [
             "Samplesheet_double_primer.tsv:md5,cd63754fefa6e844a758efb893660f97"
         ],
-        "timestamp": "2023-05-25T20:50:32+0000"
+        "timestamp": "2023-05-28T21:08:54+0000"
     },
     "cutadapt": {
         "content": [
             "cutadapt_summary.tsv:md5,ba0452e3edde6300fd111ad0e5b8e206"
         ],
-        "timestamp": "2023-05-25T20:50:32+0000"
+        "timestamp": "2023-05-28T21:08:54+0000"
     },
     "software_versions": {
         "content": [
-            {
-                "BARRNAP": {
-                    "barrnap": "0.9"
-                },
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "CUTADAPT_BASIC": {
-                    "cutadapt": "3.4"
-                },
-                "DADA2_DENOISING": {
-                    "R": "4.1.1",
-                    "dada2": "1.22.0"
-                },
-                "DADA2_FILTNTRIM": {
-                    "R": "4.1.1",
-                    "dada2": "1.22.0"
-                },
-                "DADA2_QUALITY1": {
-                    "R": "4.1.1",
-                    "ShortRead": "1.52.0",
-                    "dada2": "1.22.0"
-                },
-                "QIIME2_INSEQ": {
-                    "qiime2": "2022.11.1"
-                },
-                "RENAME_RAW_DATA_FILES": {
-                    "sed": "4.7"
-                },
-                "TRUNCLEN": {
-                    "pandas": "1.1.5",
-                    "python": "3.9.1"
-                },
-                "Workflow": {
-                    "nf-core/ampliseq": "2.6.0dev"
-                }
-            }
+            "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUTADAPT_BASIC={cutadapt=3.4}, DADA2_DENOISING={R=4.1.1, dada2=1.22.0}, DADA2_FILTNTRIM={R=4.1.1, dada2=1.22.0}, DADA2_QUALITY1={R=4.1.1, ShortRead=1.52.0, dada2=1.22.0}, QIIME2_INSEQ={qiime2=2022.11.1}, RENAME_RAW_DATA_FILES={sed=4.7}, TRUNCLEN={pandas=1.1.5, python=3.9.1}, Workflow={nf-core/ampliseq=2.6.0dev}}"
         ],
-        "timestamp": "2023-05-25T20:50:32+0000"
+        "timestamp": "2023-05-28T21:08:54+0000"
     },
     "overall_summary_tsv": {
         "content": [
             "overall_summary.tsv:md5,f0dd8c3dc3f45b84a1e32f88aabe7d08"
         ],
-        "timestamp": "2023-05-25T20:50:32+0000"
+        "timestamp": "2023-05-28T21:08:54+0000"
     },
     "dada2": {
         "content": [
@@ -68,7 +31,7 @@
             "DADA2_table.rds:md5,e527269819e4056eed063dca9f25e3e7",
             "DADA2_table.tsv:md5,d30d5d392665181abddcf8ba5bdda102"
         ],
-        "timestamp": "2023-05-25T20:50:32+0000"
+        "timestamp": "2023-05-28T21:08:54+0000"
     },
     "barrnap": {
         "content": [
@@ -77,13 +40,13 @@
             "rrna.euk.gff:md5,df19e1b84ba6f691d20c72b397c88abf",
             "rrna.mito.gff:md5,04be33c4213eb82f66cf0652fe9e32d8"
         ],
-        "timestamp": "2023-05-25T20:50:32+0000"
+        "timestamp": "2023-05-28T21:08:54+0000"
     },
     "multiqc": {
         "content": [
             "multiqc_general_stats.txt:md5,8429be0a16adf09b6634bf31b430bfac",
             "multiqc_cutadapt.txt:md5,e89359b4478ef5d10620709f651f26a2"
         ],
-        "timestamp": "2023-05-25T20:50:32+0000"
+        "timestamp": "2023-05-28T21:08:54+0000"
     }
 }
diff --git a/tests/pipeline/misc/fasta_input.nf.test b/tests/pipeline/misc/fasta_input.nf.test
@@ -14,13 +14,9 @@ nextflow_pipeline {
         }
 
         then {
-            // Remove Nextflow version from software_versions.yml
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/barrnap/rrna.arc.gff"),
                                 path("$outputDir/barrnap/rrna.bac.gff"),
                                 path("$outputDir/barrnap/rrna.euk.gff"),

diff --git a/tests/pipeline/misc/fasta_input.nf.test.snap b/tests/pipeline/misc/fasta_input.nf.test.snap
@@ -3,34 +3,19 @@
         "content": [
             "ASV_seqs.fasta:md5,39b0d4ad96b37fa68d4ee5c21b667fed"
         ],
-        "timestamp": "2023-05-25T20:48:59+0000"
+        "timestamp": "2023-05-28T21:06:17+0000"
     },
     "software_versions": {
         "content": [
-            {
-                "BARRNAP": {
-                    "barrnap": "0.9"
-                },
-                "CUSTOM_DUMPSOFTWAREVERSIONS": {
-                    "python": "3.11.0",
-                    "yaml": "6.0"
-                },
-                "DADA2_TAXONOMY": {
-                    "R": "4.1.1",
-                    "dada2": "1.22.0"
-                },
-                "Workflow": {
-                    "nf-core/ampliseq": "2.6.0dev"
-                }
-            }
+            "{BARRNAP={barrnap=0.9}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, DADA2_TAXONOMY={R=4.1.1, dada2=1.22.0}, Workflow={nf-core/ampliseq=2.6.0dev}}"
         ],
-        "timestamp": "2023-05-25T20:48:59+0000"
+        "timestamp": "2023-05-28T21:06:17+0000"
     },
     "dada2": {
         "content": [
             "ref_taxonomy.rdp_18.txt:md5,815c4fce9f3d1de019fb995a43fb66ed"
         ],
-        "timestamp": "2023-05-25T20:48:59+0000"
+        "timestamp": "2023-05-28T21:06:17+0000"
     },
     "barrnap": {
         "content": [
@@ -39,6 +24,6 @@
             "rrna.euk.gff:md5,c9bc1d9d8fb77dc19c95dee2d53840eb",
             "rrna.mito.gff:md5,df19e1b84ba6f691d20c72b397c88abf"
         ],
-        "timestamp": "2023-05-25T20:48:59+0000"
+        "timestamp": "2023-05-28T21:06:17+0000"
     }
 }
diff --git a/tests/pipeline/misc/multi_seq.nf.test b/tests/pipeline/misc/multi_seq.nf.test
@@ -14,13 +14,9 @@ nextflow_pipeline {
         }
 
         then {
-            // Remove Nextflow version from software_versions.yml
-            def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml
-            if (softwareVersions.containsKey("Workflow")) { softwareVersions.Workflow.remove("Nextflow") }
-
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(softwareVersions).match("software_versions") },
+                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") },
                 { assert snapshot(path("$outputDir/overall_summary.tsv")).match("overall_summary_tsv") },
                 { assert snapshot(path("$outputDir/barrnap/rrna.arc.gff"),
                                 path("$outputDir/barrnap/rrna.bac.gff"),