From 024e7e2c5cf16d0edf86a421eb86f6323d584731 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 22:01:44 -0600
Subject: [PATCH] Try to not error on version collect
---
.gitlab-ci.yml | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index dffe38a..5ce8c5c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -54,6 +54,11 @@ 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=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
@@ -63,7 +68,7 @@ collect:
seqtkImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f1)
seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
echo ${dir}${seqtkImg}_${seqtkVar}.sif
- singularity run ${dir}${seqtkImg}_${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt
+ singularity run ${dir}${seqtkImg}_${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt &
- >
rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1)
rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)
@@ -79,7 +84,7 @@ collect:
picardImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f1)
picardVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f2)
echo ${dir}${picardImg}_${picardVar}.sif
- singularity run ${dir}${picardImg}_${picardVar}.sif java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt
+ singularity run ${dir}${picardImg}_${picardVar}.sif java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt &
- >
subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1)
subreadVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f2)
--
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