strict syntax compatibility

.github/workflows/nf-test.yml

@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.5"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -90,7 +90,6 @@ jobs:
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test
-        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
           NXF_VERSION: ${{ matrix.NXF_VER }}

main.nf

@@ -154,16 +154,14 @@ output {
     }
     sample_vcfs {
         path { meta, vcf, tbi ->
-            def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            vcf >> "${base}.vcf.gz"
-            tbi >> "${base}.vcf.gz.tbi"
+            vcf >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz"
+            tbi >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz.tbi"
         }
     }
     family_vcfs {
         path { meta, vcf, tbi ->
-            def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            vcf >> "${base}.vcf.gz"
-            tbi >> "${base}.vcf.gz.tbi"
+            vcf >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz"
+            tbi >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz.tbi"
         }
     }
     qdnaseq_out {
@@ -186,8 +184,7 @@ output {
     }
     bedpe {
         path { meta, bedpe ->
-            def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            bedpe >> "${base}.bedpe"
+            bedpe >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".bedpe"
         }
     }
     multiqc {

modules.json

@@ -99,7 +99,7 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
+                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {

tests/lib/Utils.groovy

@@ -0,0 +1,18 @@
+import java.nio.file.Path
+import groovy.transform.CompileDynamic
+
+/**
+ * Utility functions for testing.
+ */
+@CompileDynamic
+class Utils {
+
+    static Object getRecursiveFileNames(Path fileOrDir, String outputDir) {
+        /* groovylint-disable-next-line UnnecessaryGetter */
+        if (Path.of(fileOrDir.toString()).toFile().isDirectory()) {
+            return fileOrDir.list().collect { file -> getRecursiveFileNames(file, outputDir) }
+        }
+        return fileOrDir.toString().replace("${outputDir}/", '')
+    }
+
+}

tests/pipeline/all_types/all.nf.test

@@ -27,7 +27,7 @@ nextflow_pipeline {
                     path("$outputDir")
                         .list()
                         .findAll { !it.toString().endsWith("pipeline_info") }
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                 ).match("all")}
             )
@@ -55,7 +55,7 @@ nextflow_pipeline {
                     path("$outputDir")
                         .list()
                         .findAll { !it.toString().endsWith("pipeline_info") }
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                 ).match("concat")}
             )
@@ -83,7 +83,7 @@ nextflow_pipeline {
                     path("$outputDir")
                         .list()
                         .findAll { !it.toString().endsWith("pipeline_info") }
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                 ).match("output callers")}
             )
@@ -92,10 +92,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}

tests/pipeline/bedpe/bedpe.nf.test

@@ -27,7 +27,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -79,7 +79,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -91,10 +91,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}