From 59b4661cd886f235fc7ad92d104fe098f4ba3da1 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 2 Mar 2021 21:53:17 -0600
Subject: [PATCH] Fix sif names
---
.gitlab-ci.yml | 64 +++++++++++++++++++---------------------------
version_deriva.txt | 0
2 files changed, 26 insertions(+), 38 deletions(-)
delete mode 100644 version_deriva.txt
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 33b1001..6435566 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -41,66 +41,54 @@ 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
-
+ 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
-
+ 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
-
+ 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
-
+ 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
-
+ 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)
- 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)
- echo ${dir}${rseqcImg}-${rseqcVar}.sif
- singularity run ${dir}${rseqcImg}-${rseqcVar}.sif infer_experiment.py --version > version_rseqc.txt
-
+ 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
-
+ 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)
- 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)
- 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
-
+ 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
-
+ 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
+ singularity run ${dir}${multiqcImg}_${multiqcVar}.sif multiqc --version > version_multiqc.txt
artifacts:
name: "$CI_JOB_NAME"
when: always
diff --git a/version_deriva.txt b/version_deriva.txt
deleted file mode 100644
index e69de29..0000000
--
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