diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 75a2eadb00ac207b46f8167602737e85928c34f4..1f93dcef7aced3bfb7ed15c9faadfaa59f1d0d2e 100644 --- a/.gitlab-ci.yml +++ b/.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 diff --git a/README.md b/README.md index 38d978fe4f5f2f34710591c50da10a440f5748b5..7b715d4b94ce92f8cd93806dd21bd04481f83b0a 100644 --- a/README.md +++ b/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)