Added in pipeline tracker as well as testing for astrocyte.

Removed secondary singularity version.

.gitlab-ci.yml

@@ -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

@@ -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 {
     }
 
 }
-