From 04dbe532fe98667ed08703c70169c6a8ee1fe213 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 29 Jan 2021 09:50:32 -0600
Subject: [PATCH] Change spike override to true/false
---
.gitlab-ci.yml | 2 +-
README.md | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 75a2ead..1f93dce 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 38d978f..7b715d4 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)
--
GitLab