From 76fd6d52977bb46b36eed0167ef1f8f5cce0330a Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Fri, 20 Jul 2018 15:03:10 +0200
Subject: [PATCH] Try another approach to fix the problem
---
snakecnv/align.snk | 2 +-
snakecnv/detection.snk | 2 +-
snakecnv/popsim.snk | 3 +--
snakecnv/tools/delly.snk | 3 ++-
4 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/snakecnv/align.snk b/snakecnv/align.snk
index 271f2f6..998184b 100644
--- a/snakecnv/align.snk
+++ b/snakecnv/align.snk
@@ -14,7 +14,7 @@ from align_snakemake_utils import SnakemakeUtils
# Get from config:
samples = get_samples_align(config['sample_file_align'])
-reference = os.path.abspath(config['reference'])
+reference = config['reference']
wdir = config['wdir']
workdir: wdir
diff --git a/snakecnv/detection.snk b/snakecnv/detection.snk
index 4fd2889..f4e32cc 100644
--- a/snakecnv/detection.snk
+++ b/snakecnv/detection.snk
@@ -54,7 +54,7 @@ message("Starting")
FILTERBED = get_filterbed(config)
EXCLUDEBED = get_excluded(config)
-REFERENCE = os.path.abspath(config['reference'])
+REFERENCE = config['reference']
WDIR = config['wdir']
workdir: WDIR
diff --git a/snakecnv/popsim.snk b/snakecnv/popsim.snk
index 02172ba..310e92b 100644
--- a/snakecnv/popsim.snk
+++ b/snakecnv/popsim.snk
@@ -84,8 +84,7 @@ rule get_fasta_popsim:
input:
"reference_raw.fasta"
output:
- "reference.fasta",
- os.path.join(WDIR, "reference.fasta")
+ "reference.fasta"
run:
from Bio import SeqIO
with open(input[0], "rU") as handle, open(output[0], "w") as f:
diff --git a/snakecnv/tools/delly.snk b/snakecnv/tools/delly.snk
index d6624f1..58b1d75 100644
--- a/snakecnv/tools/delly.snk
+++ b/snakecnv/tools/delly.snk
@@ -10,6 +10,7 @@ rule delly:
"{batch}/delly/delly_{chrom}_{svtype}.bcf"
params:
template = EMPTY_TEMPLATE
+ refrence = os.path.abspath(REFERENCE)
threads:
get_threads("delly", 4)
log:
@@ -18,6 +19,6 @@ rule delly:
shell:
"export OMP_NUM_THREADS={threads} ; "
"delly.py -b {input.bamlist} -c {wildcards.chrom}"
- " -g {input.reference} -x {input.excluded} -t {wildcards.svtype}"
+ " -g {params.reference} -x {input.excluded} -t {wildcards.svtype}"
" -o {output} -e {params.template}"
" 1>{log.stdout} 2>{log.stderr}"
--
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