From 3b4d0255e7f2cb51c8e4a984f20127003fbd9bf4 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 24 Mar 2020 15:39:49 -0500
Subject: [PATCH] Add dowsampling trimmed fastqs
---
workflow/conf/biohpc.config | 3 +++
workflow/nextflow.config | 3 +++
workflow/rna-seq.nf | 47 +++++++++++++++++++++++++++++++++++--
3 files changed, 51 insertions(+), 2 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 83fac1f..5bcbc27 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -18,6 +18,9 @@ process {
withName:trimData {
queue = 'super'
}
+ withName:downsampleData {
+ executor = 'local'
+ }
withName:alignData {
queue = '256GB,256GBv1'
}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index f0be347..eb9ca4d 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -26,6 +26,9 @@ process {
withName: trimData {
container = 'bicf/trimgalore:1.1'
}
+ withName: downsampleData {
+ container = 'bicf/seqtk:2.0.0'
+ }
withName: alignData {
container = 'bicf/gudmaprbkaligner:2.0.0'
}
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 2285223..625e3a0 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -117,6 +117,7 @@ process getData {
// Replicate raw fastqs for multiple process inputs
fastqs.into {
+ fastqs_downsampleData
fastqs_trimData
fastqs_fastqc
}
@@ -190,6 +191,7 @@ metadata.splitCsv(sep: ",", header: false).separate(
)
// Replicate metadata for multiple process inputs
endsManual.into {
+ endsManual_downsampleData
endsManual_trimData
endsManual_alignData
endsManual_featureCounts
@@ -284,7 +286,7 @@ process trimData {
path (fastq) from fastqs_trimData
output:
- path ("*.fq.gz") into fastqs_trimmed
+ path ("*.fq.gz") into fastqsTrim
path ("*_trimming_report.txt") into trimQC
path ("${repRID}.trimData.{out,err}")
@@ -306,6 +308,47 @@ process trimData {
"""
}
+// Replicate trimmed fastqs
+fastqsTrim.into {
+ fastqsTrim_downsampleData
+ fastqsTrim_alignData
+}
+
+/*
+ * downsampleData: downsample fastq's for metadata inference
+ */
+process downsampleData {
+ tag "${repRID}"
+ publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.downsampleData.{out,err}"
+
+ input:
+ val endsManual_downsampleData
+ path fastq from fastqsTrim_downsampleData
+
+ output:
+ path ("sampled.{1,2}.fq") into fastqsSample
+ path ("${repRID}.downsampleData.{out,err}")
+
+ script:
+ """
+ hostname > ${repRID}.downsampleData.err
+ ulimit -a >> ${repRID}.downsampleData.err
+ export https_proxy=\${http_proxy}
+
+ if [ "${endsManual_downsampleData}" == "se" ]
+ then
+ echo "LOG: downsampling single-end trimmed fastq" >> ${repRID}.downsampleData.err
+ seqtk sample -s100 *trimmed.fq.gz 10000 1> sampled.1.fq 2>> ${repRID}.downsampleData.err
+ elif [ "${endsManual_downsampleData}" == "pe" ]
+ then
+ echo "LOG: downsampling read 1 of paired-end trimmed fastq" >> ${repRID}.downsampleData.err
+ seqtk sample -s100 *1.fq.gz 1000000 1> sampled.1.fq 2>> ${repRID}.downsampleData.err
+ echo "LOG: downsampling read 2 of paired-end trimmed fastq" >> ${repRID}.downsampleData.err
+ seqtk sample -s100 *2.fq.gz 1000000 1> sampled.2.fq 2>> ${repRID}.downsampleData.err
+ fi
+ """
+}
+
/*
* alignData: aligns the reads to a reference database
*/
@@ -316,7 +359,7 @@ process alignData {
input:
val endsManual_alignData
val stranded_alignData
- path fastq from fastqs_trimmed
+ path fastq from fastqsTrim_alignData
path reference_alignData
output:
--
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