From e9fad0f0eaf42183c43625ae0fc3c609549d67e3 Mon Sep 17 00:00:00 2001 From: "Thiseas C. Lamnidis" Date: Mon, 19 Sep 2022 14:01:44 +0200 Subject: [PATCH] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 04a8c90..447ba4d 100644 --- a/README.md +++ b/README.md @@ -7,8 +7,8 @@ Automated nf-core/eager processing of Autorun output bams. - Run `prepare_eager_tsv.R` for human SG or TF data for a given sequencing batch: ```bash - prepare_eager_tsv.R -s 210429_K00233_0191_AHKJHFBBXY_Jena0014 -a SG -o eager_inputs/ -d .eva_credentials - prepare_eager_tsv.R -s 210802_K00233_0212_BHLH3FBBXY_SRdi_JR_BN -a TF -o eager_inputs/ -d .eva_credentials + prepare_eager_tsv.R -s -a SG -o eager_inputs/ -d .eva_credentials + prepare_eager_tsv.R -s -a TF -o eager_inputs/ -d .eva_credentials ``` - Run eager with the following script, which then runs on the generated TSV files: @@ -93,7 +93,7 @@ eager_inputs A wrapper shell script that goes through all TSVs in the `eager_inputs` directory, checks if a completed run exists for a given TSV, and submits/resumes an eager run for that individual if necessary. -Currently uses eager version `2.4.2` and profiles `eva,archgen,medium_data,autorun` across all runs, with the `SG` or `TF` profiles used for their respective +Currently uses eager version `2.4.5` and profiles `eva,archgen,medium_data,autorun` across all runs, with the `SG` or `TF` profiles used for their respective data types. The outputs are saved with the same directory structure as the inputs, but in a separate parent directory.