From f8219ccf8c7f35bd6fb01d02a6b538d1e4d1638a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 3 Feb 2020 21:57:19 -0600
Subject: [PATCH] Add initial fastqc
---
workflow/conf/biohpc.config | 3 +++
workflow/nextflow.config | 3 +++
workflow/rna-seq.nf | 35 ++++++++++++++++++++++++++++++++---
3 files changed, 38 insertions(+), 3 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index a17f91e..56e7e6a 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -24,6 +24,9 @@ process {
withName: dedupData {
queue = 'super'
}
+ withName: fastqc {
+ queue = 'super'
+ }
}
singularity {
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 0b6f27a..02c71af 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -32,6 +32,9 @@ process {
withName: dedupData {
container = 'bicf/picard2.21.7:2.0.0'
}
+ withName: fastqc {
+ container = 'bicf/fastqc:2.0.0'
+ }
}
trace {
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 740db3b..082e04b 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -105,6 +105,12 @@ process getData {
"""
}
+// Split fastq's
+fastqs.into {
+ fastqs_trimData
+ fastqs_fastqc
+}
+
/*
* parseMetadata: parses metadata to extract experiment parameters
*/
@@ -239,7 +245,7 @@ process trimData {
input:
val endsManual_trimData
- path (fastq) from fastqs
+ path (fastq) from fastqs_trimData
output:
path ("*.fq.gz") into fastqs_trimmed
@@ -303,7 +309,7 @@ process alignData {
}
/*
- *dedupReads: mark the duplicate reads, specifically focused on PCR or optical duplicates
+ *dedupData: mark the duplicate reads, specifically focused on PCR or optical duplicates
*/
process dedupData {
tag "${repRID}"
@@ -323,7 +329,30 @@ process dedupData {
hostname >${repRID}.dedup.err
ulimit -a >>${repRID}.dedup.err
- #Remove duplicated reads
+ # remove duplicated reads
java -jar /picard/build/libs/picard.jar MarkDuplicates I=${rawBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true 1>>${repRID}.dedup.out 2>> ${repRID}.dedup.err
"""
+}
+
+/*
+ *fastqc: run fastqc on untrimmed fastq's
+*/
+process fastqc {
+ tag "${repRID}"
+ publishDir "${logsDir}", mode: 'copy', pattern: "*.fastq.err"
+
+ input:
+ path (fastq) from fastqs_fastqc
+
+ output:
+ path ("*_fastqc.zip") into fastqc
+
+ script:
+ """
+ hostname >${repRID}.fastqc.err
+ ulimit -a >>${repRID}.fastqc.err
+
+ # run fastqc
+ fastqc *.fastq.gz >>${repRID}.fastqc.err
+ """
}
\ No newline at end of file
--
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