update doc and readme

README.md

@@ -31,14 +31,14 @@ nextflow run maxibor/coproid --genome1 'genome1.fa' --genome2 'genome2.fa' --nam
 ```
 $ nextflow run maxibor/coproid --help
 N E X T F L O W  ~  version 0.31.1
-Launching `maxibor/coproid` [stupefied_borg] - revision: f062739210
+Launching `maxibor/coproid` [confident_poincare] - revision: 4a14e6475d
 
 =========================================
  coproID: Coprolite Identification
  Homepage / Documentation: https://github.com/maxibor/coproid
  Author: Maxime Borry <borry@shh.mpg.de>
- Version 0.4
- Last updated on September 26th, 2018
+ Version 0.5
+ Last updated on September 28th, 2018
 =========================================
 Usage:
 The typical command for running the pipeline is as follows:
@@ -56,6 +56,7 @@ Options:
   --genome2                     Path to candidate 2 Coprolite maker's genome fasta file (must be surrounded with quotes)- If index2 is not set
   --index2                      Path to Bowtie2 index genome andidate 2 Coprolite maker's genome, in the form of /path/to/*.bt2 - If genome2 is not set
   --genome2Size                 Size of candidate 2 Coprolite maker's genome in bp - If genome2 is not set
+  --collapse                    Specifies if AdapterRemoval should merge the paired-end sequences or not (yes | no). Default = yes
   --identity                    Identity threshold to retain read alignment. Default = 0.85
   --bowtie                      Bowtie settings for sensivity (very-fast | very-sensitive). Default = very-sensitive
 

docs/source/index.rst

@@ -12,6 +12,7 @@ Welcome to coproID's documentation!
 
    intro
    installation
+   methods
    usage
    output
    troubleshooting

docs/source/intro.md

@@ -29,14 +29,14 @@ nextflow run maxibor/coproid --genome1 'genome1.fa' --genome2 'genome2.fa' --nam
 ```
 $ nextflow run maxibor/coproid --help
 N E X T F L O W  ~  version 0.31.1
-Launching `maxibor/coproid` [stupefied_borg] - revision: f062739210
+Launching `maxibor/coproid` [confident_poincare] - revision: 4a14e6475d
 
 =========================================
  coproID: Coprolite Identification
  Homepage / Documentation: https://github.com/maxibor/coproid
  Author: Maxime Borry <borry@shh.mpg.de>
- Version 0.4
- Last updated on September 26th, 2018
+ Version 0.5
+ Last updated on September 28th, 2018
 =========================================
 Usage:
 The typical command for running the pipeline is as follows:
@@ -54,6 +54,7 @@ Options:
   --genome2                     Path to candidate 2 Coprolite maker's genome fasta file (must be surrounded with quotes)- If index2 is not set
   --index2                      Path to Bowtie2 index genome andidate 2 Coprolite maker's genome, in the form of /path/to/*.bt2 - If genome2 is not set
   --genome2Size                 Size of candidate 2 Coprolite maker's genome in bp - If genome2 is not set
+  --collapse                    Specifies if AdapterRemoval should merge the paired-end sequences or not (yes | no). Default = yes
   --identity                    Identity threshold to retain read alignment. Default = 0.85
   --bowtie                      Bowtie settings for sensivity (very-fast | very-sensitive). Default = very-sensitive
 

docs/source/methods.md

@@ -0,0 +1,29 @@
+Methods
+=======
+
+## Pipeline overview:
+ - **0 - Fastqc:** Quality reporting on the `.fastq` files
+
+ - **1.1 - AdapterRemoval:** Adapter trimming, quality filtering, and read merging (if specified)
+
+ - **1.2 - Bowtie2:** Indexing of Genome1
+
+ - **1.3 - Bowtie2:** Indexing of Genome2
+
+ - **2.1 - Bowtie2:** Reads alignment on Genome1
+
+ - **2.2 - Bowtie2:** Reads alignment on Genome2
+
+ - **3.1 - normalizedReadCount:** Count bp aligned on Genome1 and normalise by Genome1 size -> Nnr1
+
+ - **3.2 - normalizedReadCount:** Count bp aligned on Genome2 and normalise by Genome2 size -> Nnr2
+
+ - **4 - ComputeRatio:** Compute read proportion Nnr1/Nnr2 and write Markdown report
+
+ - **5 - Pandoc:** Convert Markdown report to HTML
+
+ - **6 - MultiQC:** Generates QC report
+
+ ## Example pipeline graph
+
+ ![](_static/_img/dag.png)

docs/source/output.md

@@ -3,11 +3,15 @@ Output
 
 ## coproID results
 
- `results/{fastq_file_basename}.html`  
+ - `results/{fastq_file_basename}.html`  
 
- This file is the report of **coproID** and contains explanations on how the calculation was performed, the files used, and your result.
+    This file is the report of **coproID** and contains explanations on how the calculation were performed, the files used, and your result.
 
- An example **coproID** output file file can be found [here](_static/simulated_coprolyte.html)
+    An example **coproID** output file file can be found [here](_static/simulated_coprolyte.html)
+
+- `results/multiqc_report.html`
+
+    This file is generated by [MultiQC](http://multiqc.info/) and reports the metrics of the different tools used by **coproID**
 
 ## coproID logs
 

docs/source/usage.md

@@ -41,6 +41,11 @@ Example:
 nextflow run maxibor/coproid --genome1 'path/to/data/genomes/hsapiens.fa' --index2 'data/genomes/cfamiliaris/Bowtie2Index/*.bt2' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --genome2size 2327650711 --reads '*_R{1,2}.fastq.gz'
 ```
 
+## To collapse or not collapse
+
+Depending on the size of your DNA fragments, you might want to play with the `--collapse` option.
+You can start by leaving it to default (`--collapse yes`), and changing it to `--collapse no` if you find that most of your reads aren't merged/collapsed by `AdapterRemoval` (Plot in `multiqc` report)
+
 ## Using coproID on a cluster
 
 To use **coproID** on a cluster, you add the `-profile` option.