From 406b47beeee4900aa75dffd95ef0d35d39334d11 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 25 Apr 2020 08:22:24 -0500
Subject: [PATCH] Add trackStart process
---
workflow/conf/local.config | 11 +++++++++++
workflow/main.nf | 17 +++++++++++++++++
workflow/nextflow.config | 3 +++
3 files changed, 31 insertions(+)
diff --git a/workflow/conf/local.config b/workflow/conf/local.config
index a1e4055..ec805b0 100755
--- a/workflow/conf/local.config
+++ b/workflow/conf/local.config
@@ -1,3 +1,14 @@
process {
executor = 'local'
}
+
+singularity {
+ enabled = true
+ cacheDir = '/project/BICF/BICF_Core/shared/gudmap/singularity_cache/'
+}
+
+env {
+ http_proxy = 'http://proxy.swmed.edu:3128'
+ https_proxy = 'http://proxy.swmed.edu:3128'
+ all_proxy = 'http://proxy.swmed.edu:3128'
+}
\ No newline at end of file
diff --git a/workflow/main.nf b/workflow/main.nf
index 586dd19..cd95d38 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -77,6 +77,23 @@ outDir = params.outDir
multiqcConf = "${baseDir}/conf/multiqc_config.yaml"
references = "${baseDir}/../docs/references.md"
+/*
+ * trackStart: track start of pipeline
+ */
+process trackStart {
+ script:
+ """
+ hostname
+ ulimit -a
+ export https_proxy=\${http_proxy}
+
+ aws dynamodb put-item \
+ --table-name pipeline.tracking \
+ --item \
+ '{"sessionId": {"S": "${workflow.sessionId}"}, "pipeline": {"S": "cellranger_count"}, "projectDir": {"S": "${workflow.projectDir}"}, "start": {"S": "${workflow.start}"}, "astrocyte": {"BOOL": ${params.astrocyte}}}'
+ """
+ }
+
/*
* checkDesignFile: check design file for errors
*/
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 530f55b..20ffa62 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -14,6 +14,9 @@ profiles {
}
process {
+ withName:trackStart {
+ container = 'bicf/awscli:1.1'
+ }
withName:checkDesignFile {
container = 'bicf/python3:2.0.0'
}
--
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