From 92ed4283abfb8174f52e1ab82f32dd29b48e9ac4 Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Wed, 14 Aug 2019 14:26:12 -0500
Subject: [PATCH] Make Multiqc using singularity
---
workflow/conf/biohpc.config | 2 +-
workflow/main.nf | 7 ++-----
2 files changed, 3 insertions(+), 6 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index b213558..037d1e4 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -65,7 +65,7 @@ process {
cpus = 32
}
withName: multiqcReport {
- module = ['python/3.6.1-2-anaconda', 'pandoc/2.7', 'multiqc/1.7']
+ module = ['python/3.6.1-2-anaconda', 'pandoc/2.7', 'singularity/3.0.2']
executor = 'local'
}
}
diff --git a/workflow/main.nf b/workflow/main.nf
index f654471..bf87941 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -653,14 +653,11 @@ process multiqcReport {
script:
"""
- module load python/3.6.1-2-anaconda
- module load pandoc/2.7
- module load multiqc/1.7
echo $workflow.nextflow.version > version_nextflow.txt
- multiqc --version > version_multiqc.txt
+ singularity exec /project/shared/bicf_workflow_ref/singularity_images/multiqc.sif multiqc --version > version_multiqc.txt
python --version &> version_python.txt
python3 $baseDir/scripts/generate_references.py -r $references -o software_references
python3 $baseDir/scripts/generate_versions.py -o software_versions
- multiqc -c $multiqc .
+ singularity exec /project/shared/bicf_workflow_ref/singularity_images/multiqc.sif multiqc -c $multiqc .
"""
}
--
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