diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index 2546f71d4a11a5568fe266236e303119fc90b9cc..8e8c88c8e8d3337e140e31f2720e692aa352bb1f 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: