Sync master and develop and make a release

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 Shruti Sharma
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,5 +1,26 @@
 # gunzip_fqgz_process
 
-The nextflow wrapper for the `gunzip` process.
+## This nextflow wrapper helps to implement `gunzip` process of a `fastq` pipeline that includes:
 
-https://github.com/nextflow-hub/trimmed_gunzip_fqgz
+1. Define a default parameter `params.trimmed=true`
+2. Check if the `inputRawFilePattern` is trimmed or untrimmed
+3. The `trimmed` file has `p` in the file pattern whereas untrimmed file does not have `p` in the file pattern
+4. Based on the file pattern the input parameter of the script is defined
+5. Execute the script to gunzip the input file using `gzip –dc` command and stores the output into the `publishDir`
+
+
+## Execute the script by using the following command:
+
+```nextflow run main.nf```
+
+You will see the execution of a `gzip` process.
+
+## Execute it again adding the -resume option as shown below:
+
+```nextflow run main.nf -resume```
+
+The -resume option skips the execution of any step that has been processed in a previous execution.
+
+## Adding a publishDir directive to the gzip process to store the process results into a directory of your choice.
+
+In this script, it stores the result files locally into `results/gzip` directory.

main.nf

@@ -1,13 +1,22 @@
 #!/usr/bin/env nextflow
 
-
+/*
+#######################
+Code documentation
+#######################
+1. Define a default parameter `params.trimmed=true`
+2. Check if the `inputRawFilePattern` is trimmed or untrimmed
+3. The `trimmed` file has `p` in the file pattern whereas untrimmed file does not have `p` in the file pattern
+4. Based on the file pattern the input parameter of the script is defined
+5. Execute the script to gunzip the input file using `gzip –dc` command and stores the output into the `publishDir`
+*/
 
 /*
 ################
 params
 ################
 */
-//NOTE: default parameter
+
 params.trimmed=true
 
 
@@ -20,7 +29,7 @@ NEXTFLOW Global Config
 
 inputUntrimmedRawFilePattern = "./*_{R1,R2}.fastq.gz"
 
-//NOTE: This pipeline is starts with `trimmed` because of the `p` in the file pattern.
+
 inputTrimmedRawFilePattern = "./*_{R1,R2}.p.fastq.gz"
 
 inputRawFilePattern = params.trimmed ? inputTrimmedRawFilePattern : inputUntrimmedRawFilePattern
@@ -49,14 +58,15 @@ process gzip {
     script:
     outputExtension = params.trimmed ? '.p.fastq' : '.fastq'
 
-    // rename the output files
-    // G04880_R1.p.fastq.gz > G04880_R1.p.fastq
+    /* rename the output files
+     XYZ.p.fastq.gz  XYZ.p.fastq
+     */
     genome_1_fq = read_1_gz.name.split("\\.")[0] + outputExtension
     genome_2_fq = read_2_gz.name.split("\\.")[0] + outputExtension
 
     """
     gzip -dc ${read_1_gz} > ${genome_1_fq} 
     gzip -dc ${read_2_gz} > ${genome_2_fq}
     """
-//gzip -dc G04880_R1.p.fastq.gz > G04880_R1.p.fastq
+//gzip -dc XYZ_R1.p.fastq.gz > XYZ_R1.p.fastq
 }