add the initial code

Author: abhi18av

trimmed_gunzip.nf

@@ -0,0 +1,46 @@
+#!/usr/bin/env nextflow
+
+
+/*
+################
+NEXTFLOW Global Config
+################
+*/
+
+
+inputRawFilePattern = "./*_{R1,R2}.p.fastq.gz"
+
+Channel.fromFilePairs(inputRawFilePattern, flat: true)
+        .into { ch_in_gzip }
+
+
+/*
+################
+gzip these files
+################
+*/
+
+
+process gzip {
+    echo true
+    container 'abhi18av/biodragao_base'
+    publishDir 'results/gzip'
+
+    input:
+    tuple (genomeName, path(read_1_gz), path(read_2_gz)) from ch_in_gzip
+
+    output:
+    tuple path(genome_1_fq), path(genome_2_fq) into ch_out_gzip
+
+    script:
+    // 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'
+
+    """
+    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
+}