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BICF
Astrocyte
atacseq_analysis
Commits
ce0b51ce
Commit
ce0b51ce
authored
Jun 15, 2020
by
Venkat Malladi
Browse files
Added in pipeline tracker as well as testing for astrocyte.
Removed secondary singularity version.
parent
8a8e66b5
Pipeline
#7192
failed with stages
in 24 seconds
Changes
2
Pipelines
1
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.gitlab-ci.yml
View file @
ce0b51ce
...
...
@@ -40,5 +40,5 @@ paired_end_mouse:
-
branches
-
master
script
:
-
NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd
true
--blacklist
true
-
NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR451NAE_PE.txt" --genome 'GRCm38' --pairedEnd
true
--blacklist
true
--astrocyte
true
-
pytest -m pairedend_mouse
workflow/main.nf
View file @
ce0b51ce
...
...
@@ -50,6 +50,32 @@ gtfFile = params.gtfFile
blacklistFile = params.blacklistFile
geneNames = params.geneNames
/*
* trackStart: track start of pipeline
*/
params.ci = false
process trackStart {
script:
"""
hostname
ulimit -a
export https_proxy=\${http_proxy}
curl -H 'Content-Type: application/json' -X PUT -d '{ \
"sessionId": "${workflow.sessionId}", \
"pipeline": "${workflow.manifest.name}", \
"start": "${workflow.start}", \
"astrocyte": ${params.astrocyte}, \
"status": "started", \
"nextflowVersion": "${workflow.nextflow.version}",
"pipelineVersion": "${workflow.manifest.version}",
"ci": ${params.ci}}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
}
process checkDesignFile {
publishDir "${outDir}/design", mode: 'copy'
...
...
@@ -97,7 +123,7 @@ if (pairedEnd) {
rawReads = designFilePaths
.splitCsv(sep: '\t', header: true)
.map { row -> [ row.sample_id, [row.fastq_read1, row.fastq_read2], row.experiment_id, row.replicate, row.fq_length ] }
}
}
else {
rawReads = designFilePaths
.splitCsv(sep: '\t', header: true)
...
...
@@ -602,7 +628,7 @@ process experimentQC {
module load bedtools/2.26.0
python3 ${baseDir}/scripts/experiment_qc.py -d ${designExperimentQC} -p
bash ${baseDir}/scripts/make_tss.sh ${gtfFile}
module load singularity/
2.6.1
module load singularity/
3.0.2
singularity run /project/shared/bicf_workflow_ref/singularity_images/metaseq.simg ${baseDir}/scripts/atac_qc.py -d ${designExperimentQC} -l ${fqlengthDesign} -t gencode.tss -c ${chromSizes}
"""
}
...
...
@@ -614,7 +640,7 @@ process experimentQC {
module load bedtools/2.26.0
python3 ${baseDir}/scripts/experiment_qc.py -d ${designExperimentQC}
bash ${baseDir}/scripts/make_tss.sh ${gtfFile}
module load singularity/
2.6.1
module load singularity/
3.0.2
singularity run /project/shared/bicf_workflow_ref/singularity_images/metaseq.simg ${baseDir}/scripts/atac_qc.py -d ${designExperimentQC} -l ${fqlengthDesign} -t gencode.tss -c ${chromSizes}
"""
}
...
...
@@ -693,4 +719,3 @@ process multiqcReport {
}
}
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