From fa009e234ba01a2dad1a0df58790ca443f30fdb9 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 15 Jan 2021 09:27:50 -0600
Subject: [PATCH] Add in missinng process config.
---
docs/software_versions_mqc.yaml | 4 ++--
workflow/conf/aws.config | 5 +++++
workflow/conf/biohpc.config | 2 +-
workflow/nextflow.config | 5 ++++-
4 files changed, 12 insertions(+), 4 deletions(-)
diff --git a/docs/software_versions_mqc.yaml b/docs/software_versions_mqc.yaml
index b1982d3..c860074 100755
--- a/docs/software_versions_mqc.yaml
+++ b/docs/software_versions_mqc.yaml
@@ -6,7 +6,7 @@
description: 'are collected for pipeline version.'
data: |
<dl class="dl-horizontal">
-
+
<dt>Python</dt><dd>v3.8.3</dd>
<dt>DERIVA</dt><dd>v1.4.3</dd>
<dt>BDBag</dt><dd>v1.5.6</dd>
@@ -20,5 +20,5 @@
<dt>deepTools</dt><dd>v3.5.0</dd>
<dt>FastQC</dt><dd>v0.11.9</dd>
<dt>MultiQC</dt><dd>v1.9</dd>
- <dt>Pipeline Version</dt><dd>v1.0.1</dd>
+ <dt>Pipeline Version</dt><dd>v1.0.2</dd>
</dl>
diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
index 9a0d374..eec8a7a 100644
--- a/workflow/conf/aws.config
+++ b/workflow/conf/aws.config
@@ -116,6 +116,11 @@ process {
cpus = 1
memory = '1 GB'
}
+ withName:failPreExecutionRun_species {
+ {
+ cpus = 1
+ memory = '1 GB'
+ }
withName:failExecutionRun {
cpus = 1
memory = '1 GB'
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index a3b1632..33917db 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -85,7 +85,7 @@ process {
withName:failPreExecutionRun_fastq {
executor = 'local'
}
- withName:failPreExecutionRun {
+ withName:failPreExecutionRun_species {
executor = 'local'
}
withName:failExecutionRun {
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index b7a36ff..66b847b 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -91,6 +91,9 @@ process {
withName:failPreExecutionRun_fastq {
container = 'gudmaprbk/deriva1.4:1.0.0'
}
+ withName:failPreExecutionRun_species {
+ container = 'gudmaprbk/deriva1.4:1.0.0'
+ }
withName:failExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.0'
}
@@ -122,6 +125,6 @@ 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 = 'v1.0.1'
+ version = 'v1.0.2'
nextflowVersion = '>=19.09.0'
}
--
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