Merge pull request #12 from pphector/master

Added documentation of GenPipes proof of concept pipeline

Author: jonathangoeke

README.md

@@ -26,6 +26,7 @@ Each workflow manager folder in this repository has a README detailing how to ru
 - [Snakemake](snakemake)
 - [SciPipe](scipipe)
 - [WDL](wdl)
+- [GenPipes](genpipes)
 
 ## Online Documentation for Workflow managers
 Workflow managers have many more features which are not used in these implementations, and there are many additional workflow managers. You can read more about each workflow manager in their official documentation:

genpipes/README.md

@@ -0,0 +1,64 @@
+## About GenPipes
+
+[GenPipes](https://www.computationalgenomics.ca/genpipes/) is a flexible Python-based framework that facilitates the 
+development and deployment of multi-step workflows optimized for High-Performance Computing clusters and the cloud. 
+GenPipes comes with 13 validated and scalable pipelines for various genomics applications.
+
+## Training material and documentation
+
+- [Link to tutorial](https://genpipes.readthedocs.io/en/master/tutorials/list_tutorials.html)
+- [Link to online documentation](https://genpipes.readthedocs.io/en/master/index.html)
+- [Link to developer guide](https://genpipes.readthedocs.io/en/latest/development/dev_guide.html)
+
+## Community-developed workflows in GenPipes
+
+- [Amplicon Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_ampliconseq.html)
+- [ChIP Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_chipseq.html)
+- [CoV Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_covseq.html)
+- [DNA Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_dnaseq.html)
+- [DNA Sequencing High Coverage Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_dnaseq_highcov.html)
+- [HiC Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_hicseq.html)
+- [Illumina Run Processing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_illumina.html)
+- [Methylation Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_wgs_methylseq.html)
+- [Nanopore Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_nanopore.html)
+- [RNA Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_rnaseq.html)
+- [De-Novo RNA Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_rnaseq_denovo.html)
+- [RNA Sequencing Light Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_rnaseq_light.html)
+- [Tumor Pair Sequencing Pipeline](https://genpipes.readthedocs.io/en/latest/user_guide/pipelines/gp_tumourpair.html)
+
+## Running the proof of concept GenPipes pipeline
+
+This proof of concept pipeline is implemented in the following [branch](https://bitbucket.org/mugqic/genpipes/src/goekelab_manuscript). 
+To run this proof of concept, you need to clone the repository and change to the appropriate branch. The location of the cloned directory
+will be referred to as `$GENPIPES` in the following instructions. 
+
+1. From the cloned location, launch the pipeline using the attached [readset.txt](./readset.txt) file: 
+
+```
+python $GENPIPES/pipelines/goeke_rnaseq.py -c $GENPIPES/pipelines/goeke_rnaseq.slurm.ini --steps 1-3 --output pipeline_output --readsets readset.txt --job-scheduler slurm > run_commands.sh 
+	
+```
+ 
+2. To submit jobs to the scheduler just run the following command: 
+```
+bash run_commands.sh
+```
+
+*Notes:*
+ 
+- Please note that this proof of concept pipeline requires de-compressed fastqs to work properly
+- When running from Compute Canada or other supported GenPipes clusters, the pipeline will load software using linux modules, if running from 
+another location, use the [containerized version of GenPipes](https://genpipes.readthedocs.io/en/master/tutorials/genpipes_in_the_container.html).
+- GenPipes currently runs using python v2.7, a python v3 release is coming soon. 
+
+## Notes and Contribution
+
+This pipeline is a minimal example of a Salmon-based pipeline using GenPipes. We welcome contributions to the documentation 
+and workflow, please create an issue or submit a pull request!
+
+## How to cite GenPipes
+
+Bourgey M, Dali R, Eveleigh R, Chen KC, Letourneau L, Fillon J, Michaud M, Caron M, Sandoval J, Lefebvre F, Leveque G, Mercier E, 
+Bujold D, Marquis P, Van PT, Anderson de Lima Morais D, Tremblay J, Shao X, Henrion E, Gonzalez E, Quirion PO, Caron B, Bourque G. 
+**GenPipes: an open-source framework for distributed and scalable genomic analyses.** *Gigascience.* 2019 Jun 1;8(6):giz037. 
+doi: 10.1093/gigascience/giz037. PMID: 31185495; PMCID: PMC6559338.

genpipes/readset.txt

@@ -0,0 +1,2 @@
+Sample	Readset	Library	RunType	Run	Lane	Adapter1	Adapter2	Primer1	Primer2	QualityOffset	BED	FASTQ1	FASTQ2	BAM
+test	test_reads	test_reads	PAIRED_END	0000	1					33		../test_data/reads_1.fastq	../test_data/reads_2.fastq