test: Add UTILS functions from function guy

nf-core/eager#1063

Co-authored-by: jfy133 <[email protected]>
Co-authored-by: nvnieuwk <[email protected]>

Author: 3 people

tests/lib/UTILS.groovy

@@ -8,4 +8,38 @@ class UTILS {
         }
         return softwareVersions
     }
+
+// Recursively list all files in a directory and its sub-directories, matching a given suffix
+// TODO: use regex pattern instead of suffix?
+public static getAllFilesFromDir(dir, suffix) {
+    def output = []
+    new File(dir).eachFileRecurse() {
+        if (it.name.toString().endsWith(suffix)) {
+            output.add(it)
+        }
+    }
+    return output.sort()
+}
+// Recursively list all files names in a directory and its sub-directories, matching a given suffix, return file names
+public static getAllFileNamesFromDir(dir, suffix) {
+    def output = []
+    new File(dir).eachFileRecurse() {
+        if (it.name.toString().endsWith(suffix)) {
+            output.add(it.toString().split("/")[-1])
+        }
+    }
+    return output.sort()
+}
+
+// Recursively list all files names in a directory and its sub-directories, matching a given suffix, return if check if given string is in file
+public static checkAllFilesNamesFromDirForString(dir, suffix, string) {
+    def output = []
+    new File(dir).eachFileRecurse() {
+        if (it.name.toString().endsWith(suffix)) {
+            output.add(it.text.contains(string))
+        }
+    }
+    return output.sort()
+}
+
 }

workflows/tests/aligner/bwa.nf.test

@@ -21,23 +21,19 @@ nextflow_pipeline {
                 { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
                 { assert snapshot(
                     workflow.trace.tasks().size(),
-                    // TODO path("$outputDir/preprocessing/fastp/*.json").list(),
+                    UTILS.getAllFilesFromDir("$outputDir/preprocessing/fastp/", ".json"),
                     path("$outputDir/bwa/log").list(),
                     path("$outputDir/bwa/samtools_stats").list(),
                     path("$outputDir/quality_control/bbsplit").list(),
-                    // FIXME Empty
-                    path("$outputDir/quality_control/preseq").list().findAll { it.contains(".txt") },
-                    // process.out.outs[0][1].findAll {  file(it).name.contains('.pb')  },
+                    UTILS.getAllFilesFromDir("$outputDir/quality_control/preseq", ".txt"),
                     path("$outputDir/quality_control/rseqc/read_duplication/xls").list(),
                     path("$outputDir/quality_control/rseqc/read_duplication/rscript").list(),
                     path("$outputDir/quality_control/rseqc/infer_experiment").list(),
                     path("$outputDir/quality_control/rseqc/read_distribution").list(),
                     path("$outputDir/coverage_graphs/").list(),
-                    // FIXME Empty
-                    path("$outputDir/transcript_identification/").list().findAll { file(it.toString()).name.contains('.bed') },
                     path("$outputDir/transcript_identification/homer/cd4.bed"),
                     path("$outputDir/transcript_identification/homer/jurkat.bed"),
-                    // FIXME path("$outputDir/transcript_identification/pints/").list().findAll(),
+                    // FIXME UTILS.getAllFilesFromDir("$outputDir/transcript_identification/pints/", ".bed"),
                     path("$outputDir/transcript_identification/intersect/").list(),
                     path("$outputDir/transcript_identification/filtered/").list(),
                     // FIXME path("$outputDir/quantification/").list(),

workflows/tests/aligner/bwa.nf.test.snap

@@ -2,6 +2,14 @@
     "output_files": {
         "content": [
             134,
+            [
+                "cd4_REP1.trimmed.fastp.json:md5,bd9a3344c1591d6be4d524451f9dca53",
+                "cd4_REP2.trimmed.fastp.json:md5,bc6e3f9ff7835f220535cc393b8eb25f",
+                "cd4_REP3.trimmed.fastp.json:md5,c9c3a1dd0a2ebac77c9d7c3b0daf3790",
+                "cd4_REP4.trimmed.fastp.json:md5,c073bd26609ddca91396d0f374ec5b80",
+                "jurkat_REP1.trimmed.fastp.json:md5,329fd8e56421a196fc2ebd37ab3bc22d",
+                "jurkat_REP2.trimmed.fastp.json:md5,8bad5b02a27e5386255b998a6a69db15"
+            ],
             [
 
             ],
@@ -40,7 +48,18 @@
                 "jurkat_REP2.coverage.stats.txt:md5,b1940346719e4070091f2eef6e508f49"
             ],
             [
-                
+                "cd4_REP1.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
+                "cd4_REP1.lc_extrap.txt:md5,8633f84ccd5cc725db9af4b33edd63b0",
+                "cd4_REP2.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
+                "cd4_REP2.lc_extrap.txt:md5,3ad9e4028c3711e6d46831c10ed04200",
+                "cd4_REP3.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
+                "cd4_REP3.lc_extrap.txt:md5,25ebbeabee46caa86a4d6d82dd0091f1",
+                "cd4_REP4.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
+                "cd4_REP4.lc_extrap.txt:md5,d0df86774dd54421fd362d46faa3f937",
+                "jurkat_REP1.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
+                "jurkat_REP1.lc_extrap.txt:md5,84faa937faa88476c942f330c5762cb5",
+                "jurkat_REP2.c_curve.txt:md5,cf4743abdd355595d6ec1fb3f38e66e5",
+                "jurkat_REP2.lc_extrap.txt:md5,8ae0a77bcc59da38ec2da0fc1f973227"
             ],
             [
                 "cd4_REP1.pos.DupRate.xls:md5,a80db2d20096ca839a7847ec5b11bf75",
@@ -111,9 +130,6 @@
                 "jurkat_REP2.minus.bigWig:md5,686f719978de948f7045acc95f9d1c82",
                 "jurkat_REP2.plus.bedGraph:md5,569e8a25c9cf48d1ef953f3da77c48a1",
                 "jurkat_REP2.plus.bigWig:md5,cbe3fd38fe8f9508645bbfad83924212"
-            ],
-            [
-                
             ],
             "cd4.bed:md5,ab94918610a560772fdbec591200295f",
             "jurkat.bed:md5,41908723fa423a78476feb2e7627a3a4",
@@ -131,7 +147,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-09T17:35:32.797123474"
+        "timestamp": "2024-08-10T12:48:55.984269469"
     },
     "Should work with gzipped references": {
         "content": [