From ecbed605802026e6562295ffb428e4e220d88aa6 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@ed.ac.uk>
Date: Mon, 22 Nov 2021 09:58:23 +0000
Subject: [PATCH] Update SOP_alignment_variant_annotation.md
---
docs/SOP_alignment_variant_annotation.md | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/docs/SOP_alignment_variant_annotation.md b/docs/SOP_alignment_variant_annotation.md
index 28210ac..8f1597d 100644
--- a/docs/SOP_alignment_variant_annotation.md
+++ b/docs/SOP_alignment_variant_annotation.md
@@ -255,7 +255,7 @@ sbatch --export=PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=$SCRIPTS/trio_
```
cd $OUTPUT_DIR/${short_project_id}_${version}
-rm families/*/*.bam*
+rm families/*/*/*.bam*
```
12. Clean up. Clear the work and logs directories. Move the bcbio YAML configuration files into the results folder for the project. Retain reads for samples in families where one sample has failed QC, using a list `retain\_for\_rerun.txt`. These will likely be required for later runs, and it is simpler to regenerate config YAML files if it is not necessary to re-do symlinks/read merging.
@@ -267,6 +267,9 @@ rm -r *
cd $LOGS_DIR
rm -r *
+cd $PARAMS_DIR
+rm -r *
+
mkdir -p $OUTPUT_DIR/${short_project_id}_${version}/config/
mv $CONFIG_DIR/${short_project_id}_${version}*.yaml $OUTPUT_DIR/${short_project_id}_${version}/config/
--
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