From 1d9cb4f85d2cdb5823cf95b62c0ff260423d6837 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 29 Oct 2019 14:58:20 +0100
Subject: [PATCH] Missing update.
---
small_RNA-seq/small_RNA-seq.snakefile | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index 2546f71..8e8c88c 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -196,6 +196,7 @@ from libworkflows import get_chrom_sizes, column_converter, make_id_list_getter
from libworkflows import read_int_from_file, strip_split, file_len, last_lines, save_plot, SHELL_FUNCTIONS
from libworkflows import filter_combinator, read_feature_counts, sum_by_family, sum_feature_counts, sum_htseq_counts, warn_context
from smincludes import rules as irules
+from smwrappers import wrappers_dir
strip = str.strip
alignment_settings = {"bowtie2": "-L 6 -i S,1,0.8 -N 0"}
@@ -1012,7 +1013,7 @@ rule map_on_genome:
resources:
mem_mb=700
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
rule extract_nomap_siRNAs:
@@ -1065,7 +1066,7 @@ rule remap_on_genome:
resources:
mem_mb=700
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/map_on_genome"
+ f"file://{wrappers_dir}/map_on_genome"
def source_sam(wildcards):
@@ -1100,7 +1101,7 @@ rule sam2indexedbam:
resources:
mem_mb=4100
wrapper:
- "file:///pasteur/homes/bli/src/bioinfo_utils/snakemake_wrappers/sam2indexedbam"
+ f"file://{wrappers_dir}/sam2indexedbam"
rule compute_coverage:
--
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