From 3eab124a23cdbbad08b7cd7ec884d5a5d4049a35 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 21:55:17 -0600
Subject: [PATCH] Return echo to sif names
---
.gitlab-ci.yml | 40 ++++++++++++++++++++++++++--------------
1 file changed, 26 insertions(+), 14 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6435566..9a3a3f9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -41,53 +41,65 @@ collect:
- >
derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
+ echo ${dir}${derivaImg}_${derivaVar}.sif
singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli --version > version_deriva.txt
singularity run ${dir}${derivaImg}_${derivaVar}.sif bdbag --version > version_bdbag.txt
- - >
+
pythonImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f1)
pythonVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
+ echo ${dir}${pythonImg}_${pythonVar}.sif
singularity run ${dir}${pythonImg}_${pythonVar}.sif python3 --version > version_python.txt
- - >
+
fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1)
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)
+ echo ${dir}${trimgaloreImg}_${trimgaloreVar}.sif
singularity run ${dir}${trimgaloreImg}_${trimgaloreVar}.sif trim_galore --version > version_trimgalore.txt
- - >
+
seqtkImg=$(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)
- singularity run ${dir}${seqtkImg}_${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
- - >
+ echo ${dir}${seqtkImg}_${seqtkVar}.sif
+ 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)
+ echo ${dir}${rseqcImg}_${rseqcVar}.sif
singularity run ${dir}${rseqcImg}_${rseqcVar}.sif infer_experiment.py --version > version_rseqc.txt
- - >
+
hisatImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f1)
hisatVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f2)
+ echo ${dir}${hisatImg}_${hisatVar}.sif
singularity run ${dir}${hisatImg}_${hisatVar}.sif hisat2 --version > version_hisat2.txt
singularity run ${dir}${hisatImg}_${hisatVar}.sif samtools --version > version_samtools.txt
- - >
+
picardImg=$(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)
- singularity run ${dir}${picardImg}_${picardVar}.sif java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
- - >
+ echo ${dir}${picardImg}_${picardVar}.sif
+ 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)
+ echo ${dir}${subreadImg}_${subreadVar}.sif
singularity run ${dir}${subreadImg}_${subreadVar}.sif featureCounts -v &> version_featurecounts.txt
singularity run ${dir}${subreadImg}_${subreadVar}.sif R --version > version_r.txt
- - >
+
deeptoolsImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f1)
deeptoolsVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f2)
+ echo ${dir}${deeptoolsImg}_${deeptoolsVar}.sif
singularity run ${dir}${deeptoolsImg}_${deeptoolsVar}.sif deeptools --version > version_deeptools.txt
- - >
+
multiqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f1)
multiqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f2)
+ echo ${dir}${multiqcImg}_${multiqcVar}.sif
singularity run ${dir}${multiqcImg}_${multiqcVar}.sif multiqc --version > version_multiqc.txt
artifacts:
name: "$CI_JOB_NAME"
@@ -962,4 +974,4 @@ consistency:
paths:
- SE_multiqc_data.json
- PE_multiqc_data.json
- expire_in: 7 days
+ expire_in: 7 days
\ No newline at end of file
--
GitLab