From dea55fc2ebee73789c82bacd28a0337e99c59b4d Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Wed, 1 Aug 2018 17:57:35 +0200
Subject: [PATCH] Pindel windows: place in a subdir, remove subdir after merge
---
snakecnv/svsnakemake_utils.py | 2 +-
snakecnv/tools/pindel.snk | 11 ++++++-----
2 files changed, 7 insertions(+), 6 deletions(-)
diff --git a/snakecnv/svsnakemake_utils.py b/snakecnv/svsnakemake_utils.py
index b3421ea..d44a7f6 100644
--- a/snakecnv/svsnakemake_utils.py
+++ b/snakecnv/svsnakemake_utils.py
@@ -71,7 +71,7 @@ class SnakemakeUtils:
def get_pindel_chr_batches(self, wildcards):
inputs = []
for batch in self.chr_batches[wildcards.chrom]:
- inputs.append("{batch}/pindel/{chrbatch}/pindel_{chrom}_{svtype}.gz".format(
+ inputs.append("{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_{svtype}.gz".format(
batch=wildcards.batch, chrom=wildcards.chrom, chrbatch="-".join(map(str, batch)),
svtype=wildcards.svtype
))
diff --git a/snakecnv/tools/pindel.snk b/snakecnv/tools/pindel.snk
index 0363803..b15594e 100644
--- a/snakecnv/tools/pindel.snk
+++ b/snakecnv/tools/pindel.snk
@@ -30,9 +30,9 @@ rule pindel:
genome = REFERENCE,
fai = REFERENCE + ".fai"
output:
- "{batch}/pindel/{chrbatch}/pindel_{chrom}_D.gz",
- "{batch}/pindel/{chrbatch}/pindel_{chrom}_INV.gz",
- "{batch}/pindel/{chrbatch}/pindel_{chrom}_TD.gz",
+ "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_D.gz",
+ "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_INV.gz",
+ "{batch}/pindel/{chrom}/{chrbatch}/pindel_{chrom}_TD.gz",
threads:
get_threads("pindel", 4)
log:
@@ -50,7 +50,7 @@ rule pindel:
"""
for svtype in D TD INV RP SI LI BP CloseEndMapped INT_final;
do
- gzip -f {wildcards.batch}/pindel/{wildcards.chrbatch}/pindel_{wildcards.chrom}_${{svtype}}
+ gzip -f {wildcards.batch}/pindel/{wildcards.chrom}/{wildcards.chrbatch}/pindel_{wildcards.chrom}_${{svtype}}
done
"""
@@ -65,4 +65,5 @@ rule mergepindelbatches:
threads:
1
shell:
- "mergepindelbatches.py {output} {input} 1>{log.stdout} 2>{log.stderr}"
\ No newline at end of file
+ "mergepindelbatches.py {output} {input} 1>{log.stdout} 2>{log.stderr}; "
+ "rm -rf {wildcards.batch}/pindel/{wildcards.chrom}"
\ No newline at end of file
--
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