From 49e3be49dc29df2d55c76c7ec81a8d8e275a237e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 12 Aug 2020 15:16:31 -0500
Subject: [PATCH] Add inital output bag creation
---
workflow/conf/aws.config | 4 ++++
workflow/conf/biohpc.config | 3 +++
workflow/nextflow.config | 5 ++++-
workflow/rna-seq.nf | 26 +++++++++++++++++++++++++-
4 files changed, 36 insertions(+), 2 deletions(-)
diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
index 9ecbfb9..b5054f7 100644
--- a/workflow/conf/aws.config
+++ b/workflow/conf/aws.config
@@ -80,4 +80,8 @@ process {
cpus = 2
memory = '1 GB'
}
+ withName: outputBag {
+ cpus = 1
+ memory = '1 GB'
+ }
}
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 338cd5d..1bcf1d4 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -54,6 +54,9 @@ process {
withName: aggrQC {
executor = 'local'
}
+ withName: outputBag {
+ executor = 'local'
+ }
}
singularity {
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index db422b6..0beef33 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -67,6 +67,9 @@ process {
withName: aggrQC {
container = 'bicf/multiqc1.8:2.0.1_indev'
}
+ withName:outputBag {
+ container = 'bicf/gudmaprbkfilexfer:2.0.1_indev'
+ }
}
trace {
@@ -94,6 +97,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
mainScript = 'rna-seq.nf'
- version = 'v0.0.1'
+ version = 'v0.0.2_indev'
nextflowVersion = '>=19.09.0'
}
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 5b03e5a..7d5e1d3 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1058,4 +1058,28 @@ process aggrQC {
multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html
cp ${repRID}.multiqc_data/multiqc_data.json ${repRID}.multiqc_data.json
"""
-}
\ No newline at end of file
+}
+
+/*
+ *ouputBag: create ouputBag
+*/
+process outputBag {
+ tag "${repRID}"
+ publishDir "${outDir}/outputBag", mode: 'copy', pattern: "Replicate_${repRID}.outputBag.zip"
+
+ input:
+ path multiqc
+ path multiqcJSON
+
+ output:
+ path ("Replicate_*.zip") into outputBag
+
+ script:
+ """
+ mkdir Replicate_${repRID}.outputBag
+ cp ${multiqc} Replicate_${repRID}.outputBag
+ cp ${multiqcJSON} Replicate_${repRID}.outputBag
+ bdbag Replicate_${repRID}.outputBag --archiver zip
+ """
+}
+
--
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