added merge fastq example

conf/merge_fastq.config

@@ -0,0 +1,26 @@
+/*
+ You can go to projectDir (where the main.nf located) and start the NF pipeline like this
+ 
+ nextflow run scripts/merge_fastq.nf \
+ -profile tartu_hpc \
+ --outdir /gpfs/space/projects/alasoo/Walker_2019/fastq/ \
+ -c conf/merge_fastq.config \
+ -resume
+
+*/
+
+params {
+ singularity {
+ enabled = false
+ autoMounts = false
+ cacheDir = "$baseDir/singularity_img/"
+ }
+
+ readPaths = [
+ ['1', 'W19_1474', ['/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826555_1.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826556_1.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826557_1.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826558_1.fastq.gz']],
+ ['2', 'W19_1474', ['/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826555_2.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826556_2.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826557_2.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826558_2.fastq.gz']],
+ ['1', 'W19_1496', ['/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826559_1.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826560_1.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826561_1.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826562_1.fastq.gz']],
+ ['2', 'W19_1496', ['/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826559_2.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826560_2.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826561_2.fastq.gz','/gpfs/space/projects/alasoo/Walker_2019/fastq_raw/SRR10826562_2.fastq.gz']] 
+ ]
+}
+

scripts/merge_fastq.nf

@@ -17,7 +17,7 @@ process merge_fastq{
 
  script:
  """
- zcat $fastq_files | gzip > ${sample_id}_${read_pair}.fastq.gz
+ zcat ${fastq_files.join(' ')} | gzip > ${sample_id}_${read_pair}.fastq.gz
  """
 }