doc update

nf-core · Oct 4, 2018 · 046a171 · 046a171
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diff --git a/README.md b/README.md
@@ -28,14 +28,15 @@ 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` [irreverent_lumiere]
+Launching `maxibor/coproid` [special_laplace] - revision: b579d0002f
 
 =========================================
  coproID: Coprolite Identification
- Homepage / Documentation: https://github.com/maxibor/coproid
+ Homepage: https://github.com/maxibor/coproid
+ Documentation: https://coproid.readthedocs.io
  Author: Maxime Borry <borry@shh.mpg.de>
- Version 0.5
- Last updated on September 28th, 2018
+ Version 0.6
+ Last updated on October 4th, 2018
 =========================================
 Usage:
 The typical command for running the pipeline is as follows:
@@ -44,20 +45,16 @@ Mandatory arguments:
   --reads                       Path to input data (must be surrounded with quotes)
   --name1                       Name of candidate 1. Example: "Homo sapiens"
   --name2                       Name of candidate 2. Example: "Canis familiaris"
+  --genome1                     Path to candidate 1 Coprolite maker's genome fasta file (must be surrounded with quotes)
+  --genome2                     Path to candidate 2 Coprolite maker's genome fasta file (must be surrounded with quotes)
 
 Options:
   --phred                       Specifies the fastq quality encoding (33 | 64). Defaults to 33
-  --genome1                     Path to candidate 1 Coprolite maker's genome fasta file (must be surrounded with quotes) - Required if index1 is not set or mapdamage is activated
   --index1                      Path to Bowtie2 index genome andidate 1 Coprolite maker's genome, in the form of /path/to/*.bt2 - Required if genome1 is not set
-  --genome1Size                 Size of candidate 1 Coprolite maker's genome in bp - If genome1 is not set
-  --genome2                     Path to candidate 2 Coprolite maker's genome fasta file (must be surrounded with quotes)- Required if index2 is not set or mapdamage is activated
   --index2                      Path to Bowtie2 index genome andidate 2 Coprolite maker's genome, in the form of /path/to/*.bt2 - Required 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
+  --identity                    Identity threshold to retain read alignment. Default = 0.95
   --bowtie                      Bowtie settings for sensivity (very-fast | very-sensitive). Default = very-sensitive
-  --mapdamage                   Run mapDamage for DNA damage and aDNA authentification (yes | no). Default = yes
-
 Other options:
   --results                     Name of result directory. Defaults to ./results
   --help  --h                   Shows this help page

diff --git a/docs/source/_static/_img/dag.png b/docs/source/_static/_img/dag.png
diff --git a/docs/source/_static/coproID_result.html b/docs/source/_static/coproID_result.html
diff --git a/docs/source/_static/simulated_coprolite.html b/docs/source/_static/simulated_coprolite.html
diff --git a/docs/source/intro.md b/docs/source/intro.md
@@ -29,14 +29,15 @@ 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` [irreverent_lumiere]
+Launching `maxibor/coproid` [special_laplace] - revision: b579d0002f
 
 =========================================
  coproID: Coprolite Identification
- Homepage / Documentation: https://github.com/maxibor/coproid
+ Homepage: https://github.com/maxibor/coproid
+ Documentation: https://coproid.readthedocs.io
  Author: Maxime Borry <borry@shh.mpg.de>
- Version 0.5
- Last updated on September 28th, 2018
+ Version 0.6
+ Last updated on October 4th, 2018
 =========================================
 Usage:
 The typical command for running the pipeline is as follows:
@@ -45,20 +46,16 @@ Mandatory arguments:
   --reads                       Path to input data (must be surrounded with quotes)
   --name1                       Name of candidate 1. Example: "Homo sapiens"
   --name2                       Name of candidate 2. Example: "Canis familiaris"
+  --genome1                     Path to candidate 1 Coprolite maker's genome fasta file (must be surrounded with quotes)
+  --genome2                     Path to candidate 2 Coprolite maker's genome fasta file (must be surrounded with quotes)
 
 Options:
   --phred                       Specifies the fastq quality encoding (33 | 64). Defaults to 33
-  --genome1                     Path to candidate 1 Coprolite maker's genome fasta file (must be surrounded with quotes) - Required if index1 is not set or mapdamage is activated
   --index1                      Path to Bowtie2 index genome andidate 1 Coprolite maker's genome, in the form of /path/to/*.bt2 - Required if genome1 is not set
-  --genome1Size                 Size of candidate 1 Coprolite maker's genome in bp - If genome1 is not set
-  --genome2                     Path to candidate 2 Coprolite maker's genome fasta file (must be surrounded with quotes)- Required if index2 is not set or mapdamage is activated
   --index2                      Path to Bowtie2 index genome andidate 2 Coprolite maker's genome, in the form of /path/to/*.bt2 - Required 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
+  --identity                    Identity threshold to retain read alignment. Default = 0.95
   --bowtie                      Bowtie settings for sensivity (very-fast | very-sensitive). Default = very-sensitive
-  --mapdamage                   Run mapDamage for DNA damage and aDNA authentification (yes | no). Default = yes
-
 Other options:
   --results                     Name of result directory. Defaults to ./results
   --help  --h                   Shows this help page

diff --git a/docs/source/output.md b/docs/source/output.md
@@ -5,9 +5,9 @@ Output
 
  - `results/{fastq_file_basename}.html`  
 
-    This file is the report of **coproID** and contains explanations on how the calculation were 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 results.
 
-    An example **coproID** output file file can be found [here](_static/simulated_coprolite.html)
+    An example **coproID** output file file can be found [here](_static/coproID_result.html)
 
 - `results/multiqc_report.html`
 
@@ -19,6 +19,10 @@ Output
 
     [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`

diff --git a/img/dag.png b/img/dag.png
diff --git a/main.nf b/main.nf
@@ -33,7 +33,8 @@ def helpMessage() {
     log.info"""
     =========================================
      coproID: Coprolite Identification
-     Homepage / Documentation: https://github.com/maxibor/coproid
+     Homepage: https://github.com/maxibor/coproid
+     Documentation: https://coproid.readthedocs.io
      Author: Maxime Borry <borry@shh.mpg.de>
      Version ${version}
      Last updated on ${version_date}
@@ -64,7 +65,7 @@ def helpMessage() {
 
 
 version = "0.6"
-version_date = "October 3rd, 2018"
+version_date = "October 4th, 2018"
 
 params.phred = 33
 
@@ -77,7 +78,7 @@ params.index2 = ''
 params.name1 = ''
 params.name2 = ''
 params.collapse = 'yes'
-params.identity = 0.85
+params.identity = 0.95
 params.bowtie = 'very-sensitive'
 params.mapdamage = 'yes'
 css = baseDir+'/res/pandoc.css'