From eec3e073749ee8a89bfb58b4d51b1b65e4318300 Mon Sep 17 00:00:00 2001
From: kerimoff <kerimov.nurlan@gmail.com>
Date: Fri, 6 May 2022 11:52:31 +0300
Subject: [PATCH] added merge fastq example

---
 conf/merge_fastq.config | 26 ++++++++++++++++++++++++++
 scripts/merge_fastq.nf  |  2 +-
 2 files changed, 27 insertions(+), 1 deletion(-)
 create mode 100644 conf/merge_fastq.config

diff --git a/conf/merge_fastq.config b/conf/merge_fastq.config
new file mode 100644
index 0000000..eebfcd2
--- /dev/null
+++ b/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']]  
+  ]
+}
+
diff --git a/scripts/merge_fastq.nf b/scripts/merge_fastq.nf
index 17de321..03bbc5f 100644
--- a/scripts/merge_fastq.nf
+++ b/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
     """
 }