documentation update

docs/source/_static/coproid_result.csv

@@ -0,0 +1,3 @@
+Sample_name,Organism_name1,Organism_name2,Genome1_size,Genome2_size,nb_aDNA_bp_aligned_genome1,nb_aDNA_bp_aligned_genome2,NormalizedReadRatio
+metagenome,Bacillus_subtilis,Escherichia_coli,4215606,4686137,1453802,9104,7.471773618852114
+metagenomebis,Bacillus_subtilis,Escherichia_coli,4215606,4686137,4855,3598032,-9.380861910144272

docs/source/output.md

@@ -1,35 +1,39 @@
-Output
-======
+# Output
 
 ## coproID results
 
- - `results/{fastq_file_basename}.html`  
+-   `results/coproID_result.html`  
 
-    This file is the report of **coproID** and contains explanations on how the calculation were performed, the files used, and your results.
+     This file is the report of **coproID** and contains explanations on how the calculation were performed, the files used, and your results.
 
-    An example **coproID** output file file can be found [here](_static/coproID_result.html)
+     An example **coproID** output file file can be found [here](_static/coproID_result.html)
 
-- `results/multiqc_report.html`
+-   `results/coproid_result.csv`  
 
-    This file is generated by [MultiQC](http://multiqc.info/) and reports the metrics of the different tools used by **coproID**
+     This file contains the numerical results of **coproID**
 
-    An example **coproID** MultiQC report can be found [here](_static/multiqc_report.html)
+     An example **coproID** output file file can be found [here](_static/coproid_result.csv)
 
-- `results/mapdamage_{target_organism}/*`
+-   `results/multiqc_report.html`
 
-    [MapDamage ](https://ginolhac.github.io/mapDamage/) plots. These plots are included in the **coproID** reports.
+      This file is generated by [MultiQC](http://multiqc.info/) and reports the metrics of the different tools used by **coproID**
 
-- `results/bam/{target_organism}/*bam`
+      An example **coproID** MultiQC report can be found [here](_static/multiqc_report.html)
 
-    The filtered alignment `bam` files on each target genome
+-   `results/mapdamage_{target_organism}/*`
+
+      [MapDamage ](https://ginolhac.github.io/mapDamage/) plots. These plots are included in the **coproID** reports.
+
+-   `results/bam/{target_organism}/*bam`
+
+      The filtered alignment `bam` files on each target genome
 
 ## coproID logs
 
 You can generate a log file report of coproID run by using nextflow reporting option `-with-report`
 
 Example:
-```
-nextflow run maxibor/coproid --genome1 'path/to/data/genomes/hsapiens.fa' --genome2 'path/to/data/genomes/cfamiliaris.fa' --name1 'data/genomes/Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz' -with-report report.html
-```
 
-Here the log file will be saved as `report.html`
+    nextflow run maxibor/coproid --genome1 'path/to/data/genomes/hsapiens.fa' --genome2 'path/to/data/genomes/cfamiliaris.fa' --name1 'data/genomes/Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz' -with-report report.html
+
+This log file will be saved as `report.html`

docs/source/troubleshooting.md

@@ -1,9 +1,10 @@
-Troubleshooting
-===============
+# Troubleshooting
 
 ## Known issues
- - On Mac OS X, the nextflow log reporting (`-with-report`) may not work with Nextflow v0.31.1. This should be fixed in future Nextflow releases.
- - If the DNA damage levels are too low, mapDamage will crash.
+
+-   On Mac OS X, the nextflow log reporting (`-with-report`) may not work with Nextflow v0.31.1. This should be fixed in future Nextflow releases.
+-   If the DNA damage levels are too low, mapDamage may crash.
 
 ## Other issues
+
 If you find a specific issue, please open an [issue](https://github.com/maxibor/coproid/issues) on [GitHub](https://github.com/maxibor/coproid/issues)

docs/source/usage.md

@@ -1,45 +1,43 @@
-Usage
-=====
-
-
+# Usage
 
 ## Example usage case 1: Both reference genomes are in `fasta` format
 
 You need to specify:
-- the path the paired-end `fastq` sequencing files
-- the path to the two reference genomes `fasta` files
-- the names of the two reference species
+
+-   the path the paired-end `fastq` sequencing files
+-   the path to the two reference genomes `fasta` files
+-   the names of the two reference species
 
 Example:
-```
-nextflow run maxibor/coproid --genome1 'path/to/data/genomes/hsapiens.fa' --genome2 'path/to/data/genomes/cfamiliaris.fa' --name1 'data/genomes/Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'
-```
+
+    nextflow run maxibor/coproid --genome1 'path/to/data/genomes/hsapiens.fa' --genome2 'path/to/data/genomes/cfamiliaris.fa' --name1 'data/genomes/Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'
 
 ## Example usage case 2: Both reference genomes are indexed by bowtie2
 
 You need to specify:
-- the path the paired-end `fastq` sequencing files
-- the path to the two reference genomes `bowtie2` index files
-- the names of the two reference species
-- the genome size of the two reference species
+
+-   the path the paired-end `fastq` sequencing files
+-   the path to the two reference genomes `bowtie2` index files
+-   the names of the two reference species
+-   the genome size of the two reference species
 
 Example:
-```
-nextflow run maxibor/coproid --index1 'path/to/data/genomes/hsapiens/Bowtie2Index/*.bt2' --index2 'path/to/data/genomes/cfamiliaris/Bowtie2Index/*.bt2' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --genome1Size 3099922541 --genome2size 2327650711 --reads '*_R{1,2}.fastq.gz'
-```
+
+    nextflow run maxibor/coproid --index1 'path/to/data/genomes/hsapiens/Bowtie2Index/*.bt2' --index2 'path/to/data/genomes/cfamiliaris/Bowtie2Index/*.bt2'  --genome1 'path/to/data/genomes/hsapiens.fa' --genome2 'path/to/data/genomes/cfamiliaris.fa' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'
+
 ## Example usage case 3: One reference genome in `fasta` format, the other is indexed by bowtie2
 
 You need to specify:
-- the path the paired-end `fastq` sequencing files
-- the path the reference genomes `fasta` files
-- the path to other reference genomes `bowtie2` index files
-- the names of the two reference species
-- the genome size of the `bowtie2` indexed reference species
+
+-   the path the paired-end `fastq` sequencing files
+-   the path the reference genomes `fasta` files
+-   the path to other reference genomes `bowtie2` index files
+-   the names of the two reference species
+-   the genome size of the `bowtie2` indexed reference species
 
 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'
-```
+
+    nextflow run maxibor/coproid --genome1 'path/to/data/genomes/hsapiens.fa' --genome2 'path/to/data/genomes/cfamiliaris.fa' --index2 'data/genomes/cfamiliaris/Bowtie2Index/*.bt2' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'
 
 ## To collapse or not collapse
 
@@ -53,13 +51,11 @@ To use **coproID** on a cluster, you add the `-profile` option.
 ### On a SLURM based cluster
 
 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' -profile slurm
-```
+
+    nextflow run maxibor/coproid -profile slurm --genome1 'path/to/data/genomes/hsapiens.fa' --genome2 'path/to/data/genomes/cfamiliaris.fa' --index2 'data/genomes/cfamiliaris/Bowtie2Index/*.bt2' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'
 
 ### On SDAG
 
 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' -profile sdag
-```
+
+    nextflow run maxibor/coproid -profile sdag --genome1 'path/to/data/genomes/hsapiens.fa' --genome2 'path/to/data/genomes/cfamiliaris.fa' --index2 'data/genomes/cfamiliaris/Bowtie2Index/*.bt2' --name1 'Homo_sapiens' --name2 'Canis_familiaris' --reads '*_R{1,2}.fastq.gz'