From d275c4b32a90cfd7f56f83e9404aab02a876f2e9 Mon Sep 17 00:00:00 2001
From: Iris Mestres <iris.mestrespascual@unibas.ch>
Date: Mon, 20 Feb 2023 12:24:54 +0100
Subject: [PATCH] Add rule to create pre-miRNA annotation file
---
workflow/rules/prepare.smk | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/workflow/rules/prepare.smk b/workflow/rules/prepare.smk
index f16c715..937770f 100644
--- a/workflow/rules/prepare.smk
+++ b/workflow/rules/prepare.smk
@@ -458,6 +458,35 @@ rule gfftobed:
) &> {log}"
+###############################################################################
+### Extract pre-miRNA
+###############################################################################
+
+
+rule filter_pre_mirs:
+ input:
+ bed=os.path.join(
+ config["output_dir"], "{organism}", "mirna_filtered.bed"
+ ),
+ output:
+ bed=os.path.join(
+ config["output_dir"], "{organism}", "pre_mirna_filtered.bed"
+ ),
+ params:
+ cluster_log=os.path.join(
+ config["cluster_log"], "{organism}", "filter_pre_mirs.log"
+ ),
+ precursor="miRNA_primary_transcript",
+ log:
+ os.path.join(
+ config["local_log"], "{organism}", "filter_pre_mirs.log"
+ ),
+ singularity:
+ "docker://zavolab/ubuntu:18.04"
+ shell:
+ "(grep {params.precursor} {input.bed} > {output.bed}) &> {log}"
+
+
###############################################################################
### Extract mature miRNA
###############################################################################
@@ -580,6 +609,7 @@ rule iso_anno:
"(bedtools slop \
-i {input.bed} \
-g {input.chrsize} \
+ -s \
-l {params.bp_5p} \
-r {params.bp_3p} \
> {output.bed} \
--
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