Merge branch '39-dev.docs' into 'develop'

Resolve "Update design docs"

Closes #39

See merge request !21

.gitlab-ci.yml

@@ -89,4 +89,10 @@ integration_se:
 integration_pe:
   stage: integration
   script:
-  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA
\ No newline at end of file
+  - nextflow run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA -with-dag dag.png
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - dag.png
+    expire_in: 7 days

.gitlab/issue_templates/Bug.md

 # Summary
 
 
-# Setps to reproduce
+# Steps to reproduce
 
 
 # Observed bug behavoir
@@ -18,4 +18,4 @@
 
 
 /label ~bug ~"To Do"
-/cc @ghenry @venkat.malladi @s181706 @s189701
\ No newline at end of file
+/cc @ghenry @venkat.malladi @s181706
\ No newline at end of file

.gitlab/merge_request_templates/Merge_Request.md

-Please fill in the appropriate checklist below (delete whatever is not relevant).
-These are the most common things requested on pull requests (PRs).
+Please fill in the appropriate checklist below (delete those which are not relevant).
+These are the most common things requested on pull requests.
 
 ## PR checklist
  - [ ] This comment contains a description of changes (with reason)
  - [ ] If you've fixed a bug or added code that should be tested, add tests!
  - [ ] Documentation in `docs` is updated
+ - [ ] Replace dag.png with the most recent CI pipleine integrated_pe artifact
  - [ ] `CHANGELOG.md` is updated
  - [ ] `README.md` is updated
  - [ ] `LICENSE.md` is updated with new contributors

README.md

@@ -5,7 +5,7 @@
 [![DOI]()]()
 -->
 RNA-Seq Analytic Pipeline for GUDMAP/RBK
-===========================
+========================================
 
 Introduction
 ------------
@@ -13,17 +13,37 @@ This pipeline was created to be a standard mRNA-sequencing analysis pipeline whi
 
 ![flowchart](docs/RNA-Seq%20Pipeline%20Design%20Flowchart.jpg "Flowchart")
 
+Cloud Compatibility:
+--------------------
+This pipeline is also capable of being run on AWS. To do so:
+* Build a AWS batch queue and environment either manually or with [aws-cloudformantion](https://console.aws.amazon.com/cloudformation/home?#/stacks/new?stackName=Nextflow&templateURL=https://s3.amazonaws.com/aws-genomics-workflows/templates/nextflow/nextflow-aio.template.yaml)
+* Edit one of the aws configs in workflow/config/
+  * Replace workDir with the S3 bucket generated
+  * Change region if different
+  * Change queue to the aws batch queue generated
+* The user must have awscli configured with an appropriate authentication (with ```aws configure``` and access keys) in the environment which nextflow will be run
+* Add ```-profile ``` with the name aws config which was customized
+
 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
-  ```
+  * ```--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
+  * ```--refMoVersion``` mouse reference version ***(optional)***
+  * ```--refHuVersion``` human reference version ***(optional)***
+  * ```-profile``` config profile to use: standard = local processes on BioHPC (default), biohpc = BioHPC cluster, aws_ondemand = AWS Batch on-demand instant requests, aws_spot = AWS Batch spot instance requests ***(optional)***
+* 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
+
+FULL EXAMPLE:
+-------------
+```
+nextflow run workflow/rna-seq.nf --deriva ./data/credential.json --bdbag ./data/cookies.txt --repRID Q-Y5JA
+```
 
 
 
@@ -33,7 +53,7 @@ To Run:
 
 Credits
 =======
-This worklow is was developed by [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/)
+This workflow is was developed by [Bioinformatic Core Facility (BICF), Department of Bioinformatics](http://www.utsouthwestern.edu/labs/bioinformatics/)
 
 PI
 --
@@ -69,3 +89,11 @@ UT Southwestern Medical Center\
 [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)**.
+
+<hr>
+<hr>
+
+Pipeline Directed Acyclic Graph
+-------------------------------
+
+![dag](docs/dag.png "DAG")
\ No newline at end of file

docs/RNA-Seq Pipeline Design Flowchart.drawio

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\ No newline at end of file

workflow/rna-seq.nf

@@ -193,11 +193,9 @@ stranded.into {
 }
 spike.into{
   spike_getRef
-  spike_rseqc
 }
 species.into {
   species_getRef
-  species_rseqc
 }
 
 /*
@@ -285,7 +283,6 @@ process trimData {
 
 reference.into {
   reference_alignData
-  reference_rseqc
 }
 
 /*