Sorted file list and added activation script

nf-core · Jun 30, 2024 · 340823e · 340823e
1 parent f473a3b
commit 340823e
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Showing 3 changed files with 25 additions and 9 deletions.
diff --git a/modules/nf-core/evigene/tr2aacds/main.nf b/modules/nf-core/evigene/tr2aacds/main.nf
@@ -31,6 +31,14 @@ process EVIGENE_TR2AACDS {
 
     def simple_name = fasta.simpleName
     """
+    # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
+    # Check for container variable initialisation script and source it.
+    if [ -f "/usr/local/env-activate.sh" ]; then
+        set +u  # Otherwise, errors out because of various unbound variables
+        . "/usr/local/env-activate.sh"
+        set -u
+    fi
+
     \$EVIGENEHOME/scripts/prot/tr2aacds.pl \\
         $args \\
         -NCPU=$task.cpus \\
@@ -61,6 +69,14 @@ process EVIGENE_TR2AACDS {
         log.info '[evigene] Available memory not known - defaulting to 7GB. Specify process memory requirements to change this.'
     }
     """
+    # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
+    # Check for container variable initialisation script and source it.
+    if [ -f "/usr/local/env-activate.sh" ]; then
+        set +u  # Otherwise, errors out because of various unbound variables
+        . "/usr/local/env-activate.sh"
+        set -u
+    fi
+
     mkdir dropset
     touch dropset/${prefix}.drop.aa
     touch dropset/${prefix}.drop.cds

diff --git a/modules/nf-core/evigene/tr2aacds/tests/main.nf.test b/modules/nf-core/evigene/tr2aacds/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.dropset[0][1],
-                    file(process.out.okayset[0][1]).listFiles().collect { it.name },
+                    file(process.out.okayset[0][1]).listFiles().collect { it.name }.toSorted(),
                     process.out.versions,
                     ).match()
                 }

diff --git a/modules/nf-core/evigene/tr2aacds/tests/main.nf.test.snap b/modules/nf-core/evigene/tr2aacds/tests/main.nf.test.snap
@@ -94,18 +94,18 @@
                 "test.drop.tr:md5,5f38aa1a7e7adb09ce34c0bd74727d67"
             ],
             [
-                "test.pubids",
                 "test.ann.txt",
-                "test.pubids.realt.log",
-                "test.mainalt.tab",
-                "test.okay.aa",
-                "test.okay.mrna",
                 "test.cull.aa",
+                "test.cull.cds",
                 "test.cull.mrna",
                 "test.genesum.txt",
-                "test.cull.cds",
+                "test.mainalt.tab",
+                "test.okay.aa",
                 "test.okay.cds",
-                "test.pubids.old"
+                "test.okay.mrna",
+                "test.pubids",
+                "test.pubids.old",
+                "test.pubids.realt.log"
             ],
             [
                 "versions.yml:md5,57e8000ce92f5f8d590e7baffa762e84"
@@ -115,6 +115,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-30T13:32:04.295304"
+        "timestamp": "2024-06-30T13:46:54.373144"
     }
 }