Change spike override to true/false

.gitlab-ci.yml

@@ -891,7 +891,7 @@ 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-Y5F0 --source staging --spikeForce t --upload true --dev false --ci true --track false -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-Y5F0 --source staging --spikeForce true --upload true --dev false --ci true --track false -with-report ./spikeOverride_report.html
   - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_multiqc_data.json \;
   - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./spikeOverride_multiqc.html \;
   - pytest -m completionMultiqc --filename spikeOverride_multiqc_data.json

README.md

@@ -61,8 +61,8 @@ To Run:
     * eg: `--speciesForce 'Mus musculus'`
   * `--strandedForce` forces the strandedness to be "forward", "reverse" or "unstranded", it bypasses a metadata mismatch error
     * eg: `--strandedForce 'unstranded'`
-  * `--spikeForce` forces the spike-in to be "f" or "t", it bypasses a metadata mismatch error
-    * eg: `--spikeForce 't'`
+  * `--spikeForce` forces the spike-in to be "false" or "true", it bypasses a metadata mismatch error
+    * eg: `--spikeForce 'true'`
 * Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)):
   * `--ci` boolean (default = false)
   * `--dev` boolean (default = true)