Try making reads directory first

phac-nml · Jan 24, 2024 · 4ec4df3 · 4ec4df3
1 parent a9a9451
commit 4ec4df3
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -54,6 +54,11 @@ jobs:
         run: |
           nf-test test
 
+      - name: List test files
+        if: always()
+        run: |
+          ls -laR .nf-test/tests/*/work/*
+
       - name: Nextflow run with test profile
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
diff --git a/modules/local/sratools/fasterqdump/main.nf b/modules/local/sratools/fasterqdump/main.nf
@@ -35,17 +35,17 @@ process SRATOOLS_FASTERQDUMP {
     """
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
+    # Make directory ahead of time since otherwise
+    # fasterq-dump does not set correct permissions/owner
+    mkdir reads
+
     fasterq-dump \\
         $args \\
         --threads $task.cpus \\
         --outdir reads \\
         ${key_file} \\
         ${sra}
 
-    # Without this, I am unable to run tests for this module
-    # since I cannot access files in this directory
-    chmod a+x reads
-
     pigz \\
         $args2 \\
         --no-name \\