Updating readme and diagrams for pipelines

README.md

@@ -212,7 +212,9 @@ tradis pipeline create_plots --output_dir plots_output my_fastq_list.txt my_refe
 
 The output will be a series of directories for each fastq, containing the plot file for each sequence in the given reference,
 along with the aligned reads, and some statistics regarding transposon insertion sites both for each sample, and across
-all samples.  
+all samples.  The workflow for `tradis pipeline create_plots` is shown in this diagram:
+
+![create_plots pipeline](docs/pipeline_create_plots.png)
 
 A set of plot files can then be analysed in relation to each other using the `tradis pipeline compare` command.  For example:  
 
@@ -222,6 +224,10 @@ tradis pipeline compare --output_dir analysis_output --annotations my_annotation
   --control_files cont1.fq.gz cont2.fq.gz 
 ```
 
+The workflow for `tradis pipeline compare` is shown in this diagram:
+
+![compare pipeline](docs/pipeline_combine.png)
+
 The `tradis` tool has multiple functions, as shown below, and can also be found using the tools help message `tradis --help`:
 
 * `pipeline`

docs/pipeline_combine.pu

@@ -0,0 +1,39 @@
+@startuml
+
+split
+  -[hidden]->
+  #palegreen: embl;
+split again
+  -[hidden]->
+  #palegreen: control plot files;
+split again
+  -[hidden]->
+  #palegreen: condition plot files;
+end split
+
+:start tradis pipeline combine;
+
+:prepare embl file;
+split
+:run essentiality for control plot files;
+split again
+:run essentiality for condition plot files;
+end split
+split
+:compare figures from essentiality;
+split again
+: log fold change plot;
+: create gene report;
+end split
+
+: end tradis pipeline combine;
+
+split
+  #palegreen: gene report;
+  kill
+split again
+  #palegreen: figures;
+  kill
+end split
+
+@enduml

docs/pipeline_create_plots.pu

@@ -0,0 +1,40 @@
+@startuml
+
+split
+  -[hidden]->
+  #palegreen: reference genome;
+split again
+  -[hidden]->
+  #palegreen: fastq files;
+end split
+
+:start tradis pipeline create_plots;
+
+split
+  :samtools index reference (faidx);
+split again
+  :index reference (selected mapping tool);
+  split
+  :create plot file for fastq 1;
+  split again
+  :create plot file for fastq 2;
+  split again
+  :create plot file for fastq n;
+  end split
+  :combine stats from plot files;
+end split
+
+: end tradis pipeline create_plots;
+
+split
+  #palegreen: indexed reference;
+  kill
+split again
+  #palegreen: plot files;
+  kill
+split again
+  #palegreen: statistics;
+  kill
+end split
+
+@enduml