sync with develop (#3)

* general formatting

* add stub for the snippy core

* change the url

Author: abhi18av

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 BioDragao-Org
+Copyright (c) 2020 Abhinav Sharma (@abhi18av)
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,5 +1,56 @@
-# rdanalyzer_fq_process
+# Nextflow wrapper for `rd-analyzer` process.
 
-The nextflow wrapper for the `rdanalyzer` process.
+## Pre-requisites
 
-https://github.com/nextflow-hub/trimmed_rdanalyzer_fq
+- Nextflow
+- Docker 
+
+**NOTE** If you plan to setup a basic server, then you can refer [minimal-nextflow-setup](https://github.com/nextflow-hub/minimal-nextflow-setup)
+
+## Usage
+
+```
+nextflow run https://github.com/nextflow-hub/rd-analyzer
+```
+
+## Options
+
+
+- `filePattern`
+
+By default, the process assumes the files to follow the `*_{R1,R2}.fastq.gz` pattern, which could be customized using this option
+
+```
+nextflow run https://github.com/nextflow-hub/rd-analyzer --filePattern './*_{1,2}.fastq.gz'
+```
+
+- `resultsDir`
+
+By default, it stores the result files locally inside the `results` directory.
+
+```
+nextflow run https://github.com/nextflow-hub/rd-analyzer --resultsDir /path/to/custom/resultsDir
+```
+
+- `saveMode`
+
+By default, the pipeline publishes the results in the `resultsDir` by copying the relevant output.
+
+You can update this behavior by simply specifying the alternative such as `move` or `link` etc. 
+
+```
+nextflow run https://github.com/nextflow-hub/rd-analyzer --saveMode move
+```
+
+For more information please refer [Nextflow documentation](https://www.nextflow.io/docs/latest/process.html#publishdir)
+
+## Customizing the script
+
+The sole purpose of process wrappers in `nextflow-hub` is to keep the code small, clean and hackable with some basic knowledge of `nextflow` scripting.
+
+If you have specific requirements, you are encouraged to fork/clone and update your version to accomodate your needs. 
+
+
+## Contribution
+
+Contribution, in all forms, is most welcome!

main.nf

@@ -1,31 +1,36 @@
 #!/usr/bin/env nextflow
 
 /*
-################
-params
-################
+#==============================================
+code documentation
+#==============================================
 */
 
 
-params.saveBy = 'copy'
-
-
+/*
+#==============================================
+params
+#==============================================
+*/
 
+params.saveMode = 'copy'
+params.resultsDir = 'results/rdAnalyzer'
+params.filePattern = "./*_{R1,R2}.fastq.gz"
 
-Channel.fromFilePairs("./*_{R1,R2}.p.fastq")
+Channel.fromFilePairs(params.filePattern)
         .into { ch_in_rdanalyzer }
 
 
+
 /*
-###############
-RD-Analyzer
-###############
+#==============================================
+RD-analyzer
+#==============================================
 */
 
-
 process rdAnalyzer {
     container 'abhi18av/rdanalyzer'
-    publishDir 'results/rdAnalyzer', mode: params.saveBy
+    publishDir params.resultsDir, mode: params.saveMode
 
     input:
     set genomeFileName, file(genomeReads) from ch_in_rdanalyzer
@@ -35,9 +40,17 @@ process rdAnalyzer {
 
 
     script:
-    genomeName= genomeFileName.toString().split("\\_")[0]
+    genomeName = genomeFileName.toString().split("\\_")[0]
 
     """
     python  /RD-Analyzer/RD-Analyzer.py  -o ./${genomeName} ${genomeReads[0]} ${genomeReads[1]}
     """
 }
+
+
+
+/*
+#==============================================
+# extra
+#==============================================
+*/