From 6aa080b25f668b475be7612c5663af3d4d8c6632 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 21:59:55 -0600
Subject: [PATCH] Temp remove seqwho version
---
.gitlab-ci.yml | 5 -----
1 file changed, 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8d2c49d..dffe38a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -54,11 +54,6 @@ collect:
fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
echo ${dir}${fastqcImg}_${fastqcVar}.sif
singularity run ${dir}${fastqcImg}_${fastqcVar}.sif fastqc --version > version_fastqc.txt
- - >
- seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
- seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
- echo ${dir}${seqwhoImg}_${seqwhoVar}.sif
- singularity run ${dir}${seqwhoImg}_${seqwhoVar}.sif seqwho.py -h | grep -o Version.* > version_seqwho.txt
- >
trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
--
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