From c434dbd9610442bc1056acaaae801d77a151fc07 Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Tue, 14 Jan 2020 17:37:05 -0600 Subject: [PATCH] Update README.md --- README.md | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index b2a3fec..0cdfaa9 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,7 @@ -<!-- |*master*|*develop*| |:-:|:-:| |[](https://git.biohpc.swmed.edu/BICF/gudmap_rbk/rna-seq/commits/master)|[](https://git.biohpc.swmed.edu/BICF/gudmap_rbk/rna-seq/commits/develop)| - +<!-- [![DOI]()]() --> GUDMAP/RBK RNA-Seq Pipeline @@ -10,16 +9,19 @@ GUDMAP/RBK RNA-Seq Pipeline Introduction ------------ - +This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub. To Run: ------- * Available parameters: + * *--deriva* active ```credential.json``` file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server) + * *--bdbag* active ```cookies.txt``` file from [deriva-auth](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/Uploading-files-via-Deriva-client-tools#from-a-remote-server) + * *--repRID* mRNA-seq replicate RID\ + note: once deriva-auth is run and authenticated, the two files above are saved in ```~/.deriva/``` (see official documents from [deriva](https://github.com/informatics-isi-edu/deriva-client#installer-packages-for-windows-and-macosx) on the lifetime of the credentials) * FULL EXAMPLE: ``` - nextflow run workflow/rna-seq.nf + nextflow run workflow/rna-seq.nf --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA ``` -* Design example: -- GitLab