From f6a3d6d2555ca6a2e059704f31a78bac7abdcf5b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 25 Aug 2020 22:25:56 -0500
Subject: [PATCH] Fix fastqsForce param in CI
---
.gitlab-ci.yml | 4 ++--
README.md | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d34537d..ec09057 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -177,7 +177,7 @@ 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 --inputBagForce test_data/bag/Replicate_Q-Y5F6.zip --ci true
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/Replicate_Q-Y5F6.zip --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
@@ -191,7 +191,7 @@ override_fastq:
script:
- hostname
- ulimit -a
- - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --fastqForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --ci true
+ - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
diff --git a/README.md b/README.md
index b2aa90a..e96460d 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,7 @@ To Run:
* *current human* **38.p6.v31** = GRCh38.p12 with GENCODE annotation release 31
* ***Optional*** input overrides
* `--inputBagForce` utilizes a local replicate inputBag instead of downloading from the data-hub (still requires accurate repRID input)
- * eg: `--inputBagForce test_data/bagit/Replicate_Q-Y5F6.zip` (must be the expected bagit structure)
+ * eg: `--inputBagForce test_data/bag/Replicate_Q-Y5F6.zip` (must be the expected bag structure)
* `--fastqsForce` utilizes local fastq's instead of downloading from the data-hub (still requires accurate repRID input)
* eg: `--fastqsForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz'` (note the quotes around fastq's which must me named in the correct standard [*\*.R1.fastq.gz and/or \*.R2.fastq.gz*] and in the correct order)
* Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)):
--
GitLab