Merge branch 'GoekeLab:master' into master

Author: Hexotical

README.md

@@ -26,6 +26,7 @@ Each workflow manager folder in this repository has a README detailing how to ru
 - [Snakemake](snakemake) ⭐
 - [SciPipe](scipipe) ⭐
 - [GenPipes](genpipes) ⭐
+- [Bpipe](bpipe) ⭐
 - [WDL](wdl)
 
 
@@ -57,3 +58,4 @@ We would like to thank the following people for their contribution to this repos
 - [Samuel Lampa](https://github.com/samuell) for the [SciPipe workflow](scipipe)
 - [Marius van den Beek](https://github.com/mvdbeek) for the [Galaxy workflow](galaxy)
 - [José Héctor Gálvez López](https://github.com/pphector), Pierre-Olivier Quirion, Edouard Henrion, and Mathieu Bourgey for the [GenPipes workflow](genpipes)
+- [Simon Sadedin](https://github.com/ssadedin) for the [Bpipe workflow](bpipe)

bpipe/README.md

@@ -0,0 +1,49 @@
+# Example Bpipe Workflow
+
+[Bpipe](http://bpipe.org) is a workflow manager focused on emulating the simplicity of 
+the command line and making your pipelines look as close to the literal commands 
+that run as possible.
+
+Bpipe pipeline are written in Groovy, a scripting version of Java that enables powerful
+yet high performing DSLs to be easily developed. The definition of the workflow is 
+in the [quantify_rna.groovy](quantify_rna.groovy) file.
+
+To run this workflow, you can first install Bpipe using [SDKMan](https://sdkman.io/sdks#bpipe) 
+and then execute from within the bpipe directory:
+
+```
+bpipe run quantify_rna.groovy  ../test_data/*.fq.gz
+```
+
+**Note**: please make sure to use Bpipe 0.9.11 or higher for running the example.
+
+Please note the default configuration will run the commands on the local computer, and it 
+assumes that salmon and fastqc are available in the PATH. It is easy
+to configure Bpipe for other environments, and an example is shown in the 
+[bpipe.config](bpipe.config) file which illustrates how to configure it to run using
+PBS Torque. To run the Torque version you can tell Bpipe to use the alternative environment like
+so:
+
+```
+bpipe run --env torque  quantify_rna.groovy  ../test_data/*.fq.gz
+```
+
+If you would like to see how the HTML report that Bpipe makes looks, add the `-r` option:
+
+```
+bpipe run -r --env torque  quantify_rna.groovy  ../test_data/*.fq.gz
+```
+
+This example only uses very simple features of Bpipe. Bpipe has many more features
+which you can explore in the [documentation](http://docs.bpipe.org).
+
+Other useful commands to experiment with are:
+
+- `bpipe log` (see logs of a running pipeline)
+- `bpipe stop` (stop a running pipeline)
+- `bpipe history` (show history)
+
+
+Thanks for trying out the Bpipe example!
+
+

bpipe/bpipe.config

@@ -0,0 +1,28 @@
+
+// Default: will execute on local computer
+// Executables for FASTQC, salmon need to be in path already
+executor='local'
+memory='8g'
+
+// Example of how to customise for a different environment (torque 
+// running on HPC using modules)
+environments {
+
+    torque {
+        executor='torque'
+        account=''      // add any necessary account info
+        queue='batch'   // customize for your system
+
+        commands {
+            salmon {
+               modules="salmon"
+            }
+
+            fastqc {
+               modules="fastqc"
+            }
+        }
+    }
+}
+
+

bpipe/quantify_rna.groovy

@@ -0,0 +1,47 @@
+
+title 'Bpipe Example - RNASeq Transcript Quantification'
+
+REF='../test_data/transcriptome.fa'
+
+index_reference = {
+
+    doc 'Indexes the reference transcript fasta file'
+
+    output.dir = 'index'
+
+    produce('refseq.bin') {
+        exec """
+            salmon index -t $REF -i $output.dir
+        """
+    }
+}
+
+fastqc = {
+
+    doc 'Calculates aggregate statistics from FASTQ reads for quality control'
+
+    output.dir='qc'
+
+    exec """
+        fastqc --quiet $inputs.fq.gz  --outdir $output.dir
+    """
+}
+
+quantify = {
+
+    doc 'Counts transcripts present in reference fasta'
+
+    output.dir = 'quant'
+
+    exec """
+        salmon quant -i index -l A -1 $input1.fq.gz -2 $input2.fq.gz --validateMappings -o $output.dir
+    """
+}
+
+run {
+   index_reference + [ fastqc, quantify ]
+}
+
+
+
+

wdl/README.md

@@ -5,7 +5,7 @@ The Workflow Description Language ([WDL](https://openwdl.org/)) is a workflow sp
 - [WDL tutorials](https://support.terra.bio/hc/en-us/sections/360007347652-WDL-Tutorials)
 - [WDL documentation](https://support.terra.bio/hc/en-us/sections/360007274612-WDL-Documentation)
 
-## Community-developed workflows in snakemake
+## Community-developed workflows in WDL
 [BioWDL](https://github.com/biowdl) contains a collection of community developed pipelines written in WDL.
 
 ## Running the proof of concept WDL pipeline