|*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 =========================== 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 --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA ``` [**CHANGELOG**](https://git.biohpc.swmed.edu/BICF/gudmap_rbk/rna-seq/blob/develop/CHANGELOG.md) --- Credits ======= This worklow is was developed by [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/) PI -- Venkat S. Malladi\ *Faculty Associate & Director*\ Bioinformatics Core Facility\ UT Southwestern Medical Center\ <a href="https://orcid.org/0000-0002-0144-0564" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">orcid.org/0000-0002-0144-0564</a>\ [venkat.malladi@utsouthwestern.edu](mailto:venkat.malladi@utsouthwestern.edu) Developers ---------- Gervaise H. Henry\ *Computational Biologist*\ Department of Urology\ UT Southwestern Medical Center\ <a href="https://orcid.org/0000-0001-7772-9578" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">orcid.org/0000-0001-7772-9578</a>\ [gervaise.henry@utsouthwestern.edu](mailto:gervaise.henry@utsouthwestern.edu) Jonathan Gesell\ *Computational Biologist*\ Bioinformatics Core Facility\ UT Southwestern Medical Center\ <a href="https://orcid.org/0000-0001-5902-3299" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">orcid.org/0000-0001-5902-3299</a>\ [johnathan.gesell@utsouthwestern.edu](mailto:jonathn.gesell@utsouthwestern.edu) Jeremy A. Mathews\ *Computational Intern*\ Bioinformatics Core Facility\ UT Southwestern Medical Center\ <a href="https://orcid.org/0000-0002-2931-1430" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">orcid.org/0000-0002-2931-1430</a>\ [jeremy.mathews@utsouthwestern.edu](mailto:jeremy.mathews@utsouthwestern.edu) Please cite in publications: Pipeline was developed by BICF from funding provided by **Cancer Prevention and Research Institute of Texas (RP150596)**.