Merge branch 'develop' into '35-RSeQC'

# Conflicts:
#   .gitlab-ci.yml
#   workflow/conf/biohpc.config

.gitlab-ci.yml

@@ -97,4 +97,10 @@ 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
+  - 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
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id="74e2e168-ea6b-b213-b513-2b3c1d86103e">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</diagram></mxfile>
\ No newline at end of file

workflow/conf/biohpc.config

@@ -16,13 +16,13 @@ process {
     executor = 'local'
   }
   withName:trimData {
-    queue = '128GB,256GB,256GBv1'
+    queue = 'super'
   }
   withName:alignData {
     queue = '256GB,256GBv1'
   }
-  withName:dedupData {
-    queue = '128GB,256GB,256GBv1'
+  withName: dedupData {
+    queue = 'super'
   }
   withName:fastqc {
     queue = 'super'
@@ -30,6 +30,9 @@ process {
   withName:inferMetadata {
     queue = 'super'
   }
+  withName: makeBigWig {
+    queue = 'super'
+  }
 }
 
 singularity {

workflow/rna-seq.nf

@@ -288,7 +288,6 @@ process trimData {
 // Replicate reference for multiple process inputs
 reference.into {
   reference_alignData
-  reference_rseqc
 }
 
 /*