From e52bb115ee18bffbb9f03147ae92e530c91c8113 Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Fri, 1 May 2020 23:52:54 -0500 Subject: [PATCH] Fix SE alignSampleSummary output name --- workflow/rna-seq.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 917f199..211ff06 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -406,7 +406,7 @@ process alignSampleData { if [ "${ends}" == "se" ] then echo "LOG: running Hisat2 with single-end settings" >> ${repRID}.${ref}.alignSampleData.err - hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome -U ${fastq1} --summary-file ${repRID}.alignSampleSummary.txt --new-summary 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err + hisat2 -p `nproc` --add-chrname -S ${ref}.sampled.sam -x hisat2/genome -U ${fastq1} --summary-file ${ref}.alignSampleSummary.txt --new-summary 1>> ${repRID}.${ref}.alignSampleData.out 2>> ${repRID}.${ref}.alignSampleData.err elif [ "${ends}" == "pe" ] then echo "LOG: running Hisat2 with paired-end settings" >> ${repRID}.${ref}.alignSampleData.err -- GitLab