From 2f6b70f4f9d9f4d841c5e510a9619c653c96b6b5 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 7 Jan 2021 22:29:36 -0600
Subject: [PATCH] Update readme
---
README.md | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index 2bc84a0..6f6581c 100644
--- a/README.md
+++ b/README.md
@@ -35,8 +35,8 @@ To Run:
* **dev** = [dev.gudmap.org](dev.gudmap.org) (default, does not contain all data)
* **staging** = [staging.gudmap.org](staging.gudmap.org) (does not contain all data)
* **production** = [www.gudmap.org](www.gudmap.org) (***does contain all data***)
- * `--refMoVersion` mouse reference version ***(optional, default = 38.p6.vM22)***
- * `--refHuVersion` human reference version ***(optional, default = 38.p12.v31)***
+ * `--refMoVersion` mouse reference version ***(optional, default = 38.p6.vM25)***
+ * `--refHuVersion` human reference version ***(optional, default = 38.p13.v36)***
* `--refERCCVersion` human reference version ***(optional, default = 92)***
* `--upload` option to not upload output back to the data-hub ***(optional, default = false)***
* **true** = upload outputs to the data-hub
@@ -53,14 +53,14 @@ To Run:
* NOTES:
* 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)
* reference version consists of Genome Reference Consortium version, patch release and GENCODE annotation release # (leaving the params blank will use the default version tied to the pipeline version)
- * *current mouse* **38.p6.vM22** = GRCm38.p6 with GENCODE annotation release M22
- * *current human* **38.p6.v31** = GRCh38.p12 with GENCODE annotation release 31
+ * *current mouse* **38.p6.vM25** = GRCm38.p6 with GENCODE annotation release M25
+ * *current human* **38.p13.v36** = GRCh38.p13 with GENCODE annotation release 36
* ***Optional*** input overrides
* `--refSource` source for pulling references
* **biohpc** = source references from BICF_Core gudmap reference local location (workflow must be run on BioHPC system)
* **datahub** = source references from GUDMAP/RBK reference_table location (currently uses dev.gudmap.org)
* `--inputBagForce` utilizes a local replicate inputBag instead of downloading from the data-hub (still requires accurate repRID input)
- * eg: `--inputBagForce test_data/bag/Replicate_Q-Y5F6.zip` (must be the expected bag structure)
+ * eg: `--inputBagForce test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip` (must be the expected bag structure, this example will not work because it is a test bag)
* `--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)
* `--speciesForce` forces the species to be "Mus musculus" or "Homo sapiens", it bypasses ambiguous species error
@@ -72,7 +72,7 @@ To Run:
FULL EXAMPLE:
-------------
```
-nextflow run workflow/rna-seq.nf --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA
+nextflow run workflow/rna-seq.nf --repRID Q-Y5JA --source production --deriva ./data/credential.json --bdbag ./data/cookies.txt --dev false --upload true -profile biohpc
```
To run a set of replicates from study RID:
--
GitLab