From 4f9683e9041edd8b998a606000c3e2f3645004c7 Mon Sep 17 00:00:00 2001 From: kirtanav98 <123595850+kirtanav98@users.noreply.github.com> Date: Thu, 19 Oct 2023 14:46:44 -0400 Subject: [PATCH] Update inputs/templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl I see what you're saying. I was going off of how they were referred to in the dashboard prior. Should that be changed as well? Co-authored-by: epiercehoffman --- .../cohort_mode/cohort_mode_workspace_dashboard.md.tmpl | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/inputs/templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl b/inputs/templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl index c2c43cd33..dd4a682b3 100644 --- a/inputs/templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl +++ b/inputs/templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl @@ -198,8 +198,10 @@ Read the full MergeBatchSites documentation [here](https://github.com/broadinsti creating a cohort sample_set_set -At this point, if you are working with only one batch, delete all workflows for Modules 11-18 that are '[...]' versions to ensure that you run only the SingleBatch verions. -If you are working with more than one batch, delete all workflows for Modules 11-18 that are '[...]_SingleBatch' versions to ensure that the appropriate workflows are run. +#### Single-batch vs. Multi-batch processing +* If you only have one batch (`sample_set`), you will be using the workflows with the suffix `_SingleBatch` from `11-GenotypeBatch_SingleBatch` to `18-AnnotateVcf_SingleBatch`. We recommend deleting the workflow versions without the `_SingleBatch` suffix from `11-GenotypeBatch` to `18-AnnotateVcf` now to avoid confusion. +* If you have multiple batches (`sample_set`s), you will be using the cohort-mode versions of the workflows from `11-GenotypeBatch` onwards, which do not have the suffix `_SingleBatch`. We recommend deleting the workflow versions with the `_SingleBatch` suffix now to avoid confusion. + #### 11-GenotypeBatch Read the full GenotypeBatch documentation [here](https://github.com/broadinstitute/gatk-sv#genotype-batch).