From 22e4e121d397e878ae50575668f7a6fa1fc9549c Mon Sep 17 00:00:00 2001 From: Katherine Eaton Date: Fri, 28 Feb 2020 09:29:06 -0500 Subject: [PATCH] join notes --- README.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/README.md b/README.md index a8e07842e..d589095b3 100644 --- a/README.md +++ b/README.md @@ -91,3 +91,32 @@ nextflow run pipeline.nf \ -with-timeline -with-dag pipeline.pdf -with-report + +### Join Figuring Out +params.ncbimeta_join_first_final = "MasterFirst" +params.ncbimeta_join_first_uniq = "'BioSampleAccession BioSampleAccessionSecondary BioSampleSRAAccession'" +params.ncbimeta_join_first_accessory = "'Assembly SRA'" +params.ncbimeta_join_first_anchor = "BioSample" + +// NCBImetaJoin Second Parameters +params.ncbimeta_join_second_final = "Master" +params.ncbimeta_join_second_uniq = "'BioSampleBioProjectAccession'" +params.ncbimeta_join_second_accessory = "'BioProject'" +params.ncbimeta_join_second_anchor = "MasterFirst" + +NCBImetaJoin.py \ + --database yersinia_pestis_db.sqlite \ + --anchor BioSample \ + --accessory "Assembly SRA" \ + --final MasterFirst \ + --unique "BioSampleAccession BioSampleAccessionSecondary BioSampleSRAAccession" + +NCBImetaJoin.py \ + --database yersinia_pestis_db.sqlite \ + --anchor MasterFirst \ + --accessory BioProject \ + --final Master \ + --unique ${params.ncbimeta_join_second_uniq} + +### Perl5 Issues +export PERL5LIB=~/miniconda3/envs/phylo-env/lib/site_perl/5.26.2/