diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config index 0ea74405dd6faeb0342698df1ef8736804dda5c6..6bd7db17e68172dac3e16bba03965efa24cf815c 100755 --- a/workflow/conf/biohpc.config +++ b/workflow/conf/biohpc.config @@ -1,10 +1,10 @@ process { executor = 'slurm' - queue='super' + queue = 'super' // Process specific configuration - withLabel:getData { - executor = 'super' + withName:getData { + container = 'docker://bicf/bdbag:1.0' } } @@ -28,4 +28,19 @@ report { tower { accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f' enabled = true -} \ No newline at end of file +} + +singularity { + enabled = true + cacheDir = '/project/BICF/BICF_Core/s181706/github/gudmap/rna-seq/workflow/singularity' +} + +env { + http_proxy = "http://proxy.swmed.edu:3128" + https_proxy = "http://proxy.swmed.edu:3128" + HTTP_PROXY = "http://proxy.swmed.edu:3128" + HTTPS_PROXY = "http://proxy.swmed.edu:3128" + all_proxy = "http://proxy.swmed.edu:3128" + ALL_PROXY = "http://proxy.swmed.edu:3128" +} + diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index d839044791bc3aaccc701c9fb62099105c97205b..86e537b648edd8691f1e0c5bff59066b751a2187 100755 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -19,7 +19,7 @@ outDir = params.outDir */ process getData { publishDir "${outDir}/temp/getData", mode: "symlink" - conda "${baseDir}/conf/conda.env.bdbag.yml" +// conda "${baseDir}/conf/conda.env.bdbag.yml" input: file bdbag @@ -46,4 +46,4 @@ outDir = params.outDir sh ${baseDir}/scripts/renameFastq.sh \${study} echo LOG: fastq.gz files renamed to replicate RID """ - } \ No newline at end of file + }