Merge remote-tracking branch 'refs/remotes/origin/master'

docs/mop_consensus.rst

@@ -7,7 +7,7 @@ MOP_CONSENSUS
 .. autosummary::
    :toctree: generated
 
-This module takes as input the output from MOP_MOD with all the four worklows. It outputs the consensus of the diferent predictions running the tool `Nanoconsensus <https://github.com/ADelgadoT/NanoConsensus>`__ in parallel on each transcript for each comparison.
+This pipeline takes as input the output from MOP_MOD with all the four worklows. It outputs the consensus of the diferent predictions running the tool `Nanoconsensus <https://github.com/ADelgadoT/NanoConsensus>`__ in parallel on each transcript for each comparison.
 
 
 Input Parameters

docs/mop_mod.rst

@@ -7,7 +7,11 @@ MOP_MOD
 .. autosummary::
    :toctree: generated
 
-This module takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files and unspliced alignments to the transcriptome . It runs four different RNA detection algorithms (Epinano, Nanopolish, Tombo and Nanocompore) and it outputs the predictions generated by each one of them as individual tab-delimited files.
+This pipeline takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files and unspliced alignments to the transcriptome . It runs four different RNA detection algorithms (Epinano, Nanopolish, Tombo and Nanocompore) and it outputs the predictions generated by each one of them as individual tab-delimited files.
+
+.. image:: ../img/flow_mod.png
+  :width: 600
+  :alt: mop_mod graph
 
 Input Parameters
 ======================

docs/mop_preprocess.rst

@@ -126,6 +126,12 @@ The command line options for each tool used in the pipeline are stored within sp
 
 .. literalinclude:: ../mop_preprocess/tool_opts/drna_tool_seqtagger_opt.tsv
 
+The first column indicates the processing step as **basecalling** or **demultiplexing** etc. Some tools such as Guppy can be used for more processing steps. Several pre-compiled tool_opts files are stored within the folder **tool_opts**.
+
+.. note::
+   Readucks is run after guppy demultiplexing. It refines the demultiplexing generating different fastqs
+
+
 Model libraries for specific tools
 ====================
 The following folders are available the respective tools. Some models are already pre-installed-

docs/mop_tail.rst

@@ -7,7 +7,11 @@ MOP_TAIL
 .. autosummary::
    :toctree: generated
 
-This module takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files, alignment and assignment read ID to gene/transcript. It outputs the estimation of poly(A) tail length at read level provided by **Tailfindr**, **Nanopolish** or both. Tailfinr can be run using three modes: standard, for Nano3P-seq protocol with R9 chemistry and Nano3P-seq protocol with R10 chemistry.
+This pipeline takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files, alignment and assignment read ID to gene/transcript. It outputs the estimation of poly(A) tail length at read level provided by **Tailfindr**, **Nanopolish** or both. Tailfinr can be run using three modes: standard, for Nano3P-seq protocol with R9 chemistry and Nano3P-seq protocol with R10 chemistry.
+
+.. image:: ../img/flow_tail.png
+  :width: 600
+  :alt: mop_tail graph
 
 
 Input Parameters
@@ -71,4 +75,7 @@ Several folders are created by the pipeline within the output directory specifie
    "0154ce9c-fe6b-4ebc-bbb1-517fdc524207"	24.05	24.24	"YFL044C"
    "020cde28-970d-4710-90a5-977e4b4bbc46"	41.27	56.79	"YGL238W"
 
-If both softwares are run, an additional plot which shows the correlation of their results is generated.
+If both programs are run, an additional plot that shows the correlation of their results is generated.
+
+.. image:: ../img/mod_corr.png
+  :width: 400