From 66655043ea5ecbdf4f23dae479d0e58a2878fd3a Mon Sep 17 00:00:00 2001 From: Sarah Griffiths Date: Fri, 10 Jul 2026 09:54:04 +0000 Subject: [PATCH] Remove analysis_group mention [CW-7387] --- CHANGELOG.md | 1 + README.md | 4 ---- docs/06_pipeline_overview.md | 4 ---- 3 files changed, 1 insertion(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index aa6090b..ba25e70 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed - Incorrect strand assignment when mapping cDNA reads is fixed by using minimap2 `-ub` instead of `-uf`. +- Remove mention of analysis_group and type from `README.md` as they are not relevant for this workflow. ## [v2.0.1] diff --git a/README.md b/README.md index be7d1dd..73fd42f 100644 --- a/README.md +++ b/README.md @@ -200,10 +200,6 @@ sample aliases to be mapped to barcodes in multiplexed runs and is required for `barcode02`, and the values must be unique. + `alias` is the user-facing sample name, must be unique, must not begin with the word `barcode` and may contain only letters, numbers, `.`, `_` or `-`. -+ If a `type` column is present, it must use one of: - `test_sample`, `positive_control`, `negative_control`, or - `no_template_control`. -+ If an `analysis_group` column is present, every row must have a value. + For `--de_analysis`, the sheet must also contain the primary condition column (`condition` by default, overridable with `--condition_column`), plus any columns named in `--covariates`. diff --git a/docs/06_pipeline_overview.md b/docs/06_pipeline_overview.md index 2abc8d2..faeef1c 100644 --- a/docs/06_pipeline_overview.md +++ b/docs/06_pipeline_overview.md @@ -39,10 +39,6 @@ sample aliases to be mapped to barcodes in multiplexed runs and is required for `barcode02`, and the values must be unique. + `alias` is the user-facing sample name, must be unique, must not begin with the word `barcode` and may contain only letters, numbers, `.`, `_` or `-`. -+ If a `type` column is present, it must use one of: - `test_sample`, `positive_control`, `negative_control`, or - `no_template_control`. -+ If an `analysis_group` column is present, every row must have a value. + For `--de_analysis`, the sheet must also contain the primary condition column (`condition` by default, overridable with `--condition_column`), plus any columns named in `--covariates`.