Format fastq lines to not have descriptions

Workaround for biobakery/kneaddata#17
VEuPathDB · Feb 23, 2021 · f9d86c5 · f9d86c5
1 parent 89ae5f2
commit f9d86c5
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/bin/getFastqFromSraPaired b/bin/getFastqFromSraPaired
@@ -17,7 +17,7 @@ if [ ! -f "./${runId}.sra" ] ; then
   exit 1
 fi
 
-fastq-dump -B -I --split-files ./${runId}.sra
+fastq-dump -B --defline-seq '@$si/$ri' --defline-qual '+' --split-files ./${runId}.sra
 
 if [ ! -f "${runId}_1.fastq" -o ! -f "${runId}_2.fastq" ] ; then
   echo "fastq-dump didn't work as expected? ${runId}_{1,2}.fastq expected"

diff --git a/bin/getFastqFromSraSingle b/bin/getFastqFromSraSingle
@@ -16,7 +16,7 @@ if [ ! -f "./${runId}.sra" ] ; then
   exit 1
 fi
 
-fastq-dump -B -I --split-spot --skip-technical ./${runId}.sra
+fastq-dump -B --defline-seq '@$si' --defline-qual '+'  --split-spot --skip-technical ./${runId}.sra
 
 if [ ! -f "${runId}.fastq" ] ; then
   echo "fastq-dump didn't work as expected? ${runId}.fastq expected"