Commit 3731ead1 authored by MARIJON Pierre's avatar MARIJON Pierre

generate gfa with containment read

parent caecf3d6
......@@ -16,6 +16,7 @@ canu_paf = os.path.join(in_path, "canu_paf")
canu_gfa = canu_paf + ".gfa"
canu_paf_gfa_rename = canu_paf + "_rename.gfa"
canu_gfa_rename = canu_bog + "_rename.gfa"
canu_paf_gfa_containment_rename = canu_paf + "_rename.containment.gfa"
canu_contig_report = os.path.join(in_path, "contig_report")
......
......@@ -77,7 +77,7 @@ rule search_path:
canu2realname = canu_bog_readname,
read2contig = canu_read2tig,
contig2color = canu_contig_on_canu_paf + '.legend.csv',
canu_paf = canu_paf_gfa_rename
canu_paf = canu_paf_gfa_containment_rename
output:
result = "{prefix}_{name}_extremity_result.csv"
threads: 99
......
......@@ -38,7 +38,7 @@ rule search_path:
read2contig = canu_read2tig,
contig2color = canu_contig_on_minimap_paf + '.legend.csv',
canu_paf = canu_paf_gfa_rename,
minimap_paf = minimap_paf + ".gfa"
minimap_paf = minimap_gfa_containment
output:
result = "{prefix}_{name}_extremity_result.csv"
threads: 99
......
## File generate by minimap
minimap_paf = os.path.splitext(os.path.abspath(config["minimap_path"]))[0]
minimap_gfa_rename = minimap_paf + "_rename.gfa"
minimap_gfa_containment = minimap_paf + ".containment.gfa"
minimap_search_path_out = os.path.join(out_path, "find_path")
minimap_search_path_prefix = os.path.join(canu_search_path_out, "path_minimap")
......@@ -10,6 +10,17 @@ rule paf2gfa:
shell:
config['paf2gfa']['bin'] + " {input.paf} {output.gfa} --remove-all-containement"
rule paf2gfa_containment:
input:
paf="{filename}.paf"
output:
gfa="{filename}.containment.gfa"
shell:
config['paf2gfa']['bin'] + " {input.paf} {output.gfa}"
ruleorder: bandage_colo > bandage
rule bandage:
......
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