From 05959a63fe8355f1782121ea6f5375d8e4734f54 Mon Sep 17 00:00:00 2001 From: Stephanie Spielman Date: Wed, 11 Oct 2023 13:22:18 -0400 Subject: [PATCH] Update internal-instructions.md Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- internal-instructions.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/internal-instructions.md b/internal-instructions.md index 4a4d146f..b0dd9464 100644 --- a/internal-instructions.md +++ b/internal-instructions.md @@ -43,7 +43,8 @@ There are several flags and/or parameters which you may additionally wish to spe + `-resume`: Resume workflow from most recent checkpoint + `-with-tower`: Use `Nextflow Tower` to monitor workflow (requires separate [Nextflow Tower registration](https://tower.nf/)) + Workflow parameters: - + `--run_ids list, of, ids`: A custom list of ids (run, library, sample or project) for this run. + + `--run_ids list, of, ids`: A custom comma-separated list of ids (run, library, or sample) for this run. + + `--project list,of, project_ids`: A custom comma-separated list of project ids for this run [The default](config/profile_ccdl.config) run ids are `"SCPCR000001,SCPCS000101"`. + `--repeat_mapping`: Use this flag to repeat mapping, even if results already exist. + By default, the workflow checks whether each library has existing `alevin-fry` or `salmon` mapping results, and skips mapping for libraries with existing results.