From 89eba3358ca6cab9d78b8f9a77221900ea4633ad Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Wed, 1 Aug 2018 16:56:29 +0200
Subject: [PATCH] Move windowed files in subdir for pindel (try fixing
problem...)
---
snakecnv/svsnakemake_utils.py | 2 +-
snakecnv/tools/pindel.snk | 8 ++++----
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/snakecnv/svsnakemake_utils.py b/snakecnv/svsnakemake_utils.py
index 697d968..b3421ea 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/pindel_{chrom}_{chrbatch}_{svtype}.gz".format(
+ inputs.append("{batch}/pindel/{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 502e609..0363803 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/pindel_{chrom}_{chrbatch}_D.gz",
- "{batch}/pindel/pindel_{chrom}_{chrbatch}_INV.gz",
- "{batch}/pindel/pindel_{chrom}_{chrbatch}_TD.gz",
+ "{batch}/pindel/{chrbatch}/pindel_{chrom}_D.gz",
+ "{batch}/pindel/{chrbatch}/pindel_{chrom}_INV.gz",
+ "{batch}/pindel/{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/pindel_{wildcards.chrom}_{wildcards.chrbatch}_${{svtype}}
+ gzip -f {wildcards.batch}/pindel/{wildcards.chrbatch}/pindel_{wildcards.chrom}_${{svtype}}
done
"""
--
GitLab