Make tracking upload option

.gitlab-ci.yml

@@ -664,7 +664,7 @@ integration_se:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./SE_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./SE_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
   - pytest -m completionMultiqc --filename SE_multiqc_data.json
   artifacts:
@@ -689,7 +689,7 @@ integration_pe:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./PE_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./PE_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
   - pytest -m completionMultiqc --filename PE_multiqc_data.json
   artifacts:
@@ -716,7 +716,7 @@ failAmbiguousSpecies:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./failAmbiguousSpecies_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failAmbiguousSpecies_report.html
   retry:
     max: 0
     when:
@@ -731,7 +731,7 @@ failTrunkation:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./failTrunkation_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failTrunkation_report.html
   retry:
     max: 0
     when:
@@ -746,7 +746,7 @@ failMismatchR1R2:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./failMismatchR1R2_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failMismatchR1R2_report.html
   retry:
     max: 0
     when:
@@ -761,7 +761,7 @@ failUnexpectedMeta:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./failUnexpectedMeta_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failUnexpectedMeta_report.html
   retry:
     max: 0
     when:
@@ -776,7 +776,7 @@ failFileStructure:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source staging --upload true -with-dag dag.png --dev false --ci true -with-report ./failFileStructure_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failFileStructure_report.html
   retry:
     max: 0
     when:
@@ -791,7 +791,7 @@ override_inputBag:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true -with-report ./inputBagOverride_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true --track false -with-report ./inputBagOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
   - pytest -m completionMultiqc --filename inputBagOverride_PE_multiqc_data.json
   artifacts:
@@ -814,7 +814,7 @@ override_fastq:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6  --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true -with-report ./fastqOverride_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6  --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
   - pytest -m completionMultiqc --filename fastqOverride_PE_multiqc_data.json
   artifacts:
@@ -837,7 +837,7 @@ override_species:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --speciesForce 'Homo sapiens' --upload false --dev false --ci true -with-report ./speciesOverride_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EP --source staging --speciesForce 'Homo sapiens' --upload false --dev false --ci true --track false -with-report ./speciesOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
   - pytest -m completionMultiqc --filename speciesOverride_PE_multiqc_data.json
   artifacts:
@@ -860,7 +860,7 @@ override_stranded:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --strandedForce unstranded --upload false --dev false --ci true -with-report ./strandedOverride_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EP --source staging --strandedForce unstranded --upload false --dev false --ci true --track false -with-report ./strandedOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_PE_multiqc_data.json \;
   - pytest -m completionMultiqc --filename strandedOverride_PE_multiqc_data.json
   artifacts:
@@ -883,7 +883,7 @@ override_spike:
   script:
   - hostname
   - ulimit -a
-  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --spikeForce t --upload false --dev false --ci true -with-report ./spikeOverride_report.html
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --spikeForce t --upload false --dev false --ci true --track false -with-report ./spikeOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_PE_multiqc_data.json \;
   - pytest -m completionMultiqc --filename spikedOverride_PE_multiqc_data.json
   artifacts: