diff --git a/workflow/conf/local.config b/workflow/conf/local.config index a1e4055c4636c8282f85c0327f9742017b060ee2..ec805b0156837e24cc6b9d7e1c6c1b599074d208 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 586dd19671a2fba32b42483b58e9926e23599632..cd95d388e353a18fcacb2a308b9d7350078fc6ef 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 530f55b10e2f190960d1a22ac7cc07f0ee004d28..20ffa629e3b984589f7905579edc001e2bbe6ce4 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' }