Update MQC so works on gitpod, try to re-add original getAllFilesFrom…

…Dir (but not working - no md5swum?!)
nf-core · Jul 20, 2024 · a8dcd64 · a8dcd64
1 parent cac8152
commit a8dcd64
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Showing 9 changed files with 100 additions and 653 deletions.
diff --git a/modules.json b/modules.json
@@ -172,7 +172,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "picard/createsequencedictionary": {

diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/tests/test.nf.test b/tests/test.nf.test
@@ -27,8 +27,8 @@ nextflow_pipeline {
                     Exceptions (variable md5sums)
                 */
 
-                { assert snapshot( getAllFileNamesFromDir("$outputDir/damage_estimation/", '.txt')  ).match("damage_estimation_txt") },
-                { assert snapshot( getAllFileNamesFromDir("$outputDir/damage_estimation/", '.json') ).match("damage_estimation_json") },
+                { assert snapshot( getAllFilesFromDir("$outputDir/damage_estimation/", '.txt')  ).match("damage_estimation_txt") },
+                { assert snapshot( getAllFilesFromDir("$outputDir/damage_estimation/", '.json') ).match("damage_estimation_json") },
                 { assert snapshot( getAllFileNamesFromDir("$outputDir/damage_estimation/", '.svg')  ).match("damage_estimation_svg") },
                 { assert snapshot( getAllFileNamesFromDir("$outputDir/damage_estimation/", '.pdf')  ).match("damage_estimation_pdf") },
                 { assert snapshot( checkAllFilesNamesFromDirForString("$outputDir/damage_estimation/", '.log', 'FINISHED SUCCESSFULLY')  ).match("damage_estimation_log") },
@@ -46,6 +46,17 @@ nextflow_pipeline {
 }
 
 // Recursively list all files in a directory and its subdirectories matching a given suffix
+def getAllFilesFromDir(dir, suffix) {
+    def output = []
+    new File(dir).eachFileRecurse() {
+        if (it.name.toString().matches(".*\\.${suffix}")) {
+            output.add(file(it))
+        }
+    }
+    return output
+}
+
+// Recursively list all files names in a directory and its subdirectories matching a given suffix
 def getAllFileNamesFromDir(dir, suffix) {
     def output = []
     new File(dir).eachFileRecurse() {
@@ -70,7 +81,7 @@ def checkAllFilesNamesFromDirForString(dir, suffix, string) {
 //def getAllFilesFromDir(dir, suffix) {
 //    def output = []
 //    new File(dir).eachFileRecurse() {
-//        if (it.name.toString().matches(".*\\.(${suffix.join('|')})")) {
+//        if (it.name.toString().matches(".*\\.${suffix}")) {
 //            output.add(it)
 //        }
 //    }