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GUDMAP_RBK
RNA-seq
Commits
ff2f89f0
Commit
ff2f89f0
authored
4 years ago
by
Gervaise Henry
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Add quotes around img name
parent
469ef281
2 merge requests
!76
Develop
,
!71
Seqwho
Pipeline
#9394
canceled with stages
in 6 seconds
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.gitlab-ci.yml
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.gitlab-ci.yml
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ff2f89f0
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@@ -42,65 +42,65 @@ 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)
img=$(echo ${dir}${derivaImg}-${derivaVar}.sif)
singularity run ${img} deriva-download-cli --version > version_deriva.txt
singularity run ${img} bdbag --version > version_bdbag.txt
singularity run
"
${img}
"
deriva-download-cli --version > version_deriva.txt
singularity run
"
${img}
"
bdbag --version > version_bdbag.txt
-
>
pythonImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f1)
pythonVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
img=$(${dir}${pythonImg}-${pythonVar}.sif)
singularity run ${img} python3 --version > version_python.txt
singularity run
"
${img}
"
python3 --version > version_python.txt
-
>
fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1)
fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${fastqcImg}-${fastqcVar}.sif)
singularity run ${img} fastqc --version > version_fastqc.txt
singularity run
"
${img}
"
fastqc --version > version_fastqc.txt
-
>
seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
img=$(${dir}${seqwhoImg}-${seqwhoVar}.sif)
singularity run ${img} seqwho.py -h | grep -o Version.* > version_seqwho.txt
singularity run
"
${img}
"
seqwho.py -h | grep -o Version.* > version_seqwho.txt
-
>
trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${trimgaloreImg}-${trimgaloreVar}.sif)
singularity run ${img} trim_galore --version > version_trimgalore.txt
singularity run
"
${img}
"
trim_galore --version > version_trimgalore.txt
-
>
seqtkImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f1)
seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${seqtkImg}-${seqtkVar}.sif)
singularity run ${img} seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
singularity run
"
${img}
"
seqtk 2>&1 | grep -o Version.* > version_seqtk.txt&
-
>
rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1)
rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${rseqcImg}-${rseqcVar}.sif)
singularity run ${img} infer_experiment.py --version > version_rseqc.txt
singularity run
"
${img}
"
infer_experiment.py --version > version_rseqc.txt
-
>
hisatImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f1)
hisatVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${hisatImg}-${hisatVar}.sif)
singularity run ${img} hisat2 --version > version_hisat2.txt
singularity run ${img} samtools --version > version_samtools.txt
singularity run
"
${img}
"
hisat2 --version > version_hisat2.txt
singularity run
"
${img}
"
samtools --version > version_samtools.txt
-
>
picardImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f1)
picardVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${picardImg}-${picardVar}.sif)
singularity run ${img} java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
singularity run
"
${img}
"
java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
-
>
subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1)
subreadVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${subreadImg}-${subreadVar}.sif)
singularity run ${img} featureCounts -v &> version_featurecounts.txt
singularity run ${img} R --version > version_r.txt
singularity run
"
${img}
"
featureCounts -v &> version_featurecounts.txt
singularity run
"
${img}
"
R --version > version_r.txt
-
>
deeptoolsImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f1)
deeptoolsVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${deeptoolsImg}-${deeptoolsVar}.sif)
singularity run ${img} deeptools --version > version_deeptools.txt
singularity run
"
${img}
"
deeptools --version > version_deeptools.txt
-
>
multiqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f1)
multiqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f2)
img=$(echo ${dir}${multiqcImg}-${multiqcVar}.sif)
singularity run ${img} multiqc --version > version_multiqc.txt
singularity run
"
${img}
"
multiqc --version > version_multiqc.txt
artifacts
:
name
:
"
$CI_JOB_NAME"
when
:
always
...
...
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