From d4f13ebfff9b421bd36dbc6001669078adc2369a Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Sun, 8 May 2022 16:46:52 +0200
Subject: [PATCH] refactor: create new settings input

---
 modules/sratools/fasterqdump/main.nf | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/modules/sratools/fasterqdump/main.nf b/modules/sratools/fasterqdump/main.nf
index 1980ffeb..6351efd2 100644
--- a/modules/sratools/fasterqdump/main.nf
+++ b/modules/sratools/fasterqdump/main.nf
@@ -9,6 +9,7 @@ process SRATOOLS_FASTERQDUMP {
 
     input:
     tuple val(meta), path(sra)
+    path(ncbi_settings)
 
     output:
     tuple val(meta), path(output), emit: reads
@@ -20,16 +21,13 @@ process SRATOOLS_FASTERQDUMP {
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
     // Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
     // *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
     // for unpaired reads which we ignore here.
     output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
     """
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
+    if [[ "${ncbi_settings.name}" != "EXISTS" ]]; then
+        export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
     fi
 
     fasterq-dump \\