New release

README.md

@@ -0,0 +1,5 @@
+# gunzip_fqgz_process
+
+The nextflow wrapper for the `gunzip` process.
+
+https://github.com/nextflow-hub/trimmed_gunzip_fqgz

main.nf

@@ -1,14 +1,29 @@
 #!/usr/bin/env nextflow
 
 
+
+/*
+################
+params
+################
+*/
+//NOTE: default parameter
+params.trimmed=true
+
+
 /*
 ################
 NEXTFLOW Global Config
 ################
 */
 
 
-inputRawFilePattern = "./*_{R1,R2}.p.fastq.gz"
+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
 
 Channel.fromFilePairs(inputRawFilePattern, flat: true)
         .into { ch_in_gzip }
@@ -22,7 +37,6 @@ gzip these files
 
 
 process gzip {
-    echo true
     container 'abhi18av/biodragao_base'
     publishDir 'results/gzip'
 
@@ -33,10 +47,12 @@ process gzip {
     tuple path(genome_1_fq), path(genome_2_fq) into ch_out_gzip
 
     script:
+    outputExtension = params.trimmed ? '.p.fastq' : '.fastq'
+
     // rename the output files
     // G04880_R1.p.fastq.gz > G04880_R1.p.fastq
-    genome_1_fq = read_1_gz.name.split("\\.")[0] + '.p.fastq'
-    genome_2_fq = read_2_gz.name.split("\\.")[0] + '.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}