Commit ce0b51ce authored by Venkat Malladi's avatar Venkat Malladi

Added in pipeline tracker as well as testing for astrocyte.

Removed secondary singularity version.
parent 8a8e66b5
Pipeline #7192 failed with stages
in 24 seconds
......@@ -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
......@@ -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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