From c46684c37d7b70a4d6e255357844abcc07de6a90 Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Thu, 4 Apr 2019 09:20:35 +0200
Subject: [PATCH] IMAGE_vqsr : add bcftools stat output in final output list
and define final temp file to remove
---
Snakemake/IMAGE_vqsr/Snakefile | 25 ++++++++++++++++++-------
1 file changed, 18 insertions(+), 7 deletions(-)
diff --git a/Snakemake/IMAGE_vqsr/Snakefile b/Snakemake/IMAGE_vqsr/Snakefile
index 2b0499a..fe963bb 100644
--- a/Snakemake/IMAGE_vqsr/Snakefile
+++ b/Snakemake/IMAGE_vqsr/Snakefile
@@ -89,9 +89,8 @@ final_outputs.append("results/VQSR/" + gatk_prefix +"_vqsr_SNP.vcf.gz")
final_outputs.append("results/VQSR/" + gatk_prefix +"_vqsr_INDEL.vcf.gz")
final_outputs.append("results/genoFilter/" + gatk_prefix +"_vqsr_SNP_genFiltered.vcf.gz")
final_outputs.append("results/genoFilter/" + gatk_prefix +"_vqsr_INDEL_genFiltered.vcf.gz")
-final_outputs.append("results/bcftools_stats/" + gatk_prefix +"_vqsr_SNP_genFiltered.stat")
-final_outputs.append("results/bcftools_stats/" + gatk_prefix +"_vqsr_INDEL_genFiltered.stat")
-
+final_outputs.append("results/bcftools_stats/" + gatk_prefix +"_vqsr_SNP_genFiltered.stats")
+final_outputs.append("results/bcftools_stats/" + gatk_prefix +"_vqsr_INDEL_genFiltered.stats")
#~ print(final_outputs)
rule all:
@@ -103,17 +102,29 @@ onsuccess:
if not "--notemp" in sys.argv :
temp_list = list()
print("remove remained temporary file :\n")
+
+ # uniq variants
+ for caller in ["gatk","freebayes","mpileup"] :
+ temp_list.append("results/intersect/uniq_"+caller+"_variants.vcf.gz.tbi")
+ temp_list.append("results/intersect/VQSR_trainingSet_untrusted_uniquely_called_variants.vcf.gz.tbi")
+
+ # common variants
+ temp_list.append('results/intersect/common_variants.vcf.gz.tbi')
+ temp_list.append('results/hard_filtering/common_SNP_tagged.vcf.gz.tbi')
+ temp_list.append('results/hard_filtering/common_INDEL_tagged.vcf.gz.tbi')
+
# splited VCF files, except for uniquely called training set
for prefix in trainingSets:
if prefix != 'VQSR_trainingSet_trusted_3callers_hardFiltered_variants' and prefix != 'VQSR_trainingSet_untrusted_uniquely_called_variants':
temp_list.append("results/split_SNP_INDEL/" + prefix + "_SNP.vcf.gz")
temp_list.append("results/split_SNP_INDEL/" + prefix + "_INDEL.vcf.gz")
- #temp_list.append("results/split_SNP_INDEL/" + prefix + "_SNP.vcf.gz.tbi")
- #temp_list.append("results/split_SNP_INDEL/" + prefix + "_INDEL.vcf.gz.tbi")
+ temp_list.append("results/split_SNP_INDEL/" + prefix + "_SNP.vcf.gz.tbi")
+ temp_list.append("results/split_SNP_INDEL/" + prefix + "_INDEL.vcf.gz.tbi")
+
temp_list.append('results/split_SNP_INDEL/common_SNP.vcf.gz')
temp_list.append('results/split_SNP_INDEL/common_INDEL.vcf.gz')
- #temp_list.append('results/split_SNP_INDEL/common_SNP.vcf.gz.tbi')
- #temp_list.append('results/split_SNP_INDEL/common_INDEL.vcf.gz.tbi')
+ temp_list.append('results/split_SNP_INDEL/common_SNP.vcf.gz.tbi')
+ temp_list.append('results/split_SNP_INDEL/common_INDEL.vcf.gz.tbi')
for f in temp_list:
print(f)
--
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