From 4ec4df3951a4fcf01c19be560136419c7dbbbe32 Mon Sep 17 00:00:00 2001
From: Aaron Petkau <aaron.petkau@gmail.com>
Date: Wed, 24 Jan 2024 12:55:52 -0600
Subject: [PATCH] Try making reads directory first

---
 .github/workflows/ci.yml                   | 5 +++++
 modules/local/sratools/fasterqdump/main.nf | 8 ++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 03e1016..3ae2a6e 100644
--- 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 ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
diff --git a/modules/local/sratools/fasterqdump/main.nf b/modules/local/sratools/fasterqdump/main.nf
index 18c4ae1..ea055c5 100644
--- a/modules/local/sratools/fasterqdump/main.nf
+++ b/modules/local/sratools/fasterqdump/main.nf
@@ -35,6 +35,10 @@ process SRATOOLS_FASTERQDUMP {
     """
     export NCBI_SETTINGS="\$PWD/${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 \\
@@ -42,10 +46,6 @@ process SRATOOLS_FASTERQDUMP {
         ${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 \\