Merge branch '84-tracking' into 'dev'

Add in pipelinetracking.

See merge request !70

.gitlab-ci.yml

@@ -39,7 +39,7 @@ single_end_mouse:
   only:
     - master
   script:
-  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --astrocyte true --ci true --dev true
   - pytest -m singleend
 
 paired_end_human:
@@ -49,7 +49,7 @@ paired_end_human:
   except:
     - master
   script:
-  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false --ci true --dev true
   - pytest -m pairedend
 
 single_end_single_control:
@@ -59,7 +59,7 @@ single_end_single_control:
   except:
     - master
   script:
-  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false --ci true --dev true
   - pytest -m singlecontrol
 
 single_end_diff:
@@ -67,7 +67,7 @@ single_end_diff:
   only:
     - master
   script:
-  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false --ci true --dev true
   - pytest -m singleend
   - pytest -m singlediff
 
@@ -78,7 +78,7 @@ paired_end_diff:
     - master
   stage: multiple
   script:
-  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -with-dag flowchart.pdf
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -with-dag flowchart.pdf --ci true --dev true
   - pytest -m pairedend
   - pytest -m paireddiff
   artifacts:
@@ -93,7 +93,7 @@ single_end_skip:
   only:
     - master
   script:
-  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false
+  - NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false --ci true --dev true
   - pytest -m singleskip_true
 
 cleanup_job:

workflow/main.nf

@@ -28,6 +28,9 @@ params.skipMotif = false
 params.skipPlotProfile = false
 params.references = "$baseDir/../docs/references.md"
 params.multiqc =  "$baseDir/conf/multiqc_config.yaml"
+params.ci = false
+params.dev = false
+
 
 // Assign variables if astrocyte
 if (params.astrocyte) {
@@ -101,6 +104,31 @@ multiqc = params.multiqc
 gtfFile = params.gtf
 geneNames = params.geneNames
 
+/*
+ * trackStart: track start of pipeline
+ */
+
+process trackStart {
+  script:
+  """
+  hostname
+  ulimit -a
+
+  curl -H 'Content-Type: application/json' -X PUT -d '{ \
+      "sessionId": "${workflow.sessionId}", \
+      "pipeline": "chipseq_analysis", \
+      "start": "${workflow.start}", \
+      "astrocyte": ${params.astrocyte}, \
+      "status": "started", \
+      "nextflowVersion": "${workflow.nextflow.version}", \
+      "pipelineVersion": "1.1.1", \
+      "ci": ${params.ci}, \
+      "dev": ${params.dev}}' \
+  "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
+  """
+}
+
+
 // Check design file for errors
 process checkDesignFile {