From 0b5ebc9daa8cf7e2681e775c4ff90333e28c7328 Mon Sep 17 00:00:00 2001
From: Kedi Cao <kedic715@gmail.com>
Date: Tue, 4 Mar 2025 17:29:46 +0100
Subject: [PATCH] re-arrange rules
---
snakemodules/genotype.smk | 25 -------------------------
snakemodules/position.smk | 25 +++++++++++++++++++++++++
2 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/snakemodules/genotype.smk b/snakemodules/genotype.smk
index dc8c009..8eff668 100644
--- a/snakemodules/genotype.smk
+++ b/snakemodules/genotype.smk
@@ -1,28 +1,3 @@
-import os
-rule sort_vcf:
- input:
- RESULTS_DIR + "/place-finish.done",
- ins=RESULTS_DIR + "/insertions_unsorted.vcf"
- output:
- temp(RESULTS_DIR + "/insertions.vcf")
- conda:
- os.path.join(WORKFLOW_PATH,"snakemodules/envs/bcftools.yml")
- resources:
- mem_mb = resources["standard_2G"]["mem"],
- runtime = resources["standard_2G"]["time"]
- threads:
- threads["single"]
- log:
- out="logs/genotype/sort_vcf.out",
- err="logs/genotype/sort_vcf.err"
- benchmark:
- "benchmarks/genotype/sort_vcf.txt"
- shell:
- "bcftools sort {input.ins} "
- " --output-file {output}"
- " --output-type v"
- " > {log.out} 2> {log.err}"
-
rule popins2_genotype:
input:
diff --git a/snakemodules/position.smk b/snakemodules/position.smk
index 2cdd0a1..5c9d5ce 100644
--- a/snakemodules/position.smk
+++ b/snakemodules/position.smk
@@ -156,4 +156,29 @@ rule popins2_place_finish:
" --prefix {WORK_DIR} "
" --insertions {rules.popins2_place_refalign.output.vcf}"
" --reference {REFERENCE} "
+ " > {log.out} 2> {log.err}"
+
+
+rule sort_vcf:
+ input:
+ RESULTS_DIR + "/place-finish.done",
+ ins=RESULTS_DIR + "/insertions_unsorted.vcf"
+ output:
+ temp(RESULTS_DIR + "/insertions.vcf")
+ conda:
+ os.path.join(WORKFLOW_PATH,"snakemodules/envs/bcftools.yml")
+ resources:
+ mem_mb = resources["standard_2G"]["mem"],
+ runtime = resources["standard_2G"]["time"]
+ threads:
+ threads["single"]
+ log:
+ out="logs/genotype/sort_vcf.out",
+ err="logs/genotype/sort_vcf.err"
+ benchmark:
+ "benchmarks/genotype/sort_vcf.txt"
+ shell:
+ "bcftools sort {input.ins} "
+ " --output-file {output}"
+ " --output-type v"
" > {log.out} 2> {log.err}"
\ No newline at end of file
--
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