From 0eee8782e68ac40f4f345ade6a2f83e756c35bc1 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 4 Aug 2020 09:43:33 -0500
Subject: [PATCH] Fix echo greps
---
.gitlab-ci.yml | 2 +-
workflow/rna-seq.nf | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6264f76..9cceb49 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -107,7 +107,7 @@ countData:
script:
- singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' -o Q-Y5F6_1M.se.featureCounts -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
- singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.featureCounts
- - assignedReads=grep -m 1 'Assigned' *.countData.summary | grep -oe '\([0-9.]*\)'
+ - assignedReads=$(grep -m 1 'Assigned' *.countData.summary | grep -oe '\([0-9.]*\)')
- pytest -m makeFeatureCounts
makeBigWig:
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index bcdcb8b..dc0a8d1 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -877,7 +877,7 @@ process countData {
echo -e "LOG: counted" >> ${repRID}.countData.log
# extract assigned reads
- assignedReads=grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)'
+ assignedReads=\$(grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)')
echo -e \${assignedReads} > assignedReads.csv
echo -e "LOG: assigned reads: "\${assignedReads} >> ${repRID}.countData.log
--
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