From 19195674d578b54f649cb9f059567483ac1b52bd Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Fri, 3 Jan 2020 15:15:25 -0600
Subject: [PATCH] Initial branch commit
---
workflow/conf/biohpc.config | 10 +++++++---
workflow/rna-seq.nf | 16 +++++++++++++++-
2 files changed, 22 insertions(+), 4 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 5842b58..732ddb8 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -5,13 +5,17 @@ process {
// Process specific configuration
withName:splitData {
- container = 'docker://bicf/bdbag:1.0'
+ container = 'docker://bicf/gudmaprbkfilexfer:1.1'
}
withName:getData {
- container = 'docker://bicf/bdbag:1.0'
+ container = 'docker://bicf/gudmaprbkfilexfer:1.1'
}
withName:trimData {
- container = 'docker://bicf/trimgalore:1.0'
+ container = 'docker://bicf/trimgalore:1.1'
+ queue = '256GB,256GBv1,384GB'
+ }
+ withName:alignReads {
+ container = 'docker://bicf/hisat2:1.0'
queue = '256GB,256GBv1,384GB'
}
}
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 035faa8..df727d5 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -3,6 +3,8 @@
// Define input variables
params.deriva = "/project/BICF/BICF_Core/shared/gudmap/cookies/deriva-cookies.txt"
params.bdbag = "${baseDir}/../test_data/Study_Q-Y4H0.zip"
+params.spikein = "false"
+params.species = "human"
params.outDir = "${baseDir}/../output"
@@ -92,7 +94,7 @@ process trimData {
set repID, reads from trimming
output:
- path ("*_val_{1,2}.fq.gz", type: 'file', maxDepth: '0')
+ set repID, path ("*_val_{1,2}.fq.gz", type: 'file', maxDepth: '0') into aligning
script:
"""
@@ -100,3 +102,15 @@ process trimData {
trim_galore --gzip --max_n 1 --paired --basename \${rep} -j `nproc` ${reads[0]} ${reads[1]} 1>>\${rep}.trimData.log 2>>\${rep}.trimData.err;
"""
}
+
+/*
+ * alignReads: aligns the reads to a reference database
+*/
+process alignReads {
+ tag "align-${repID}"
+ publishDir "${outDir}/tempOut/aligned", mode: "symlink"
+
+ input:
+ set repID, fqs from aligning
+
+
--
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