Commit 5e8430e4 authored by MARIJON Pierre's avatar MARIJON Pierre

Use version without any overlap of containment

parent d200f04f
......@@ -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_gfa_containment_internal
minimap_paf = minimap_gfa
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 = minimap_paf + ".gfa"
minimap_gfa_rename = minimap_paf + "_rename.gfa"
minimap_gfa_containment = minimap_paf + ".containment.gfa"
minimap_gfa_containment_internal = minimap_paf + ".containment.internal.gfa"
......
import os
ruleorder: paf2gfa > paf2gfa_containment > paf2gfa_containment_internal
rule paf2gfa:
input:
paf="{filename}.paf"
......@@ -8,7 +10,7 @@ rule paf2gfa:
gfa="{filename}.gfa"
shell:
config['paf2gfa']['bin'] + " {input.paf} {output.gfa} --remove-all-internal"
config['paf2gfa']['bin'] + " {input.paf} {output.gfa} --remove-all-containment --remove-all-internal"
rule paf2gfa_containment:
input:
......@@ -18,7 +20,7 @@ rule paf2gfa_containment:
gfa="{filename}.containment.gfa"
shell:
config['paf2gfa']['bin'] + " {input.paf} {output.gfa}"
config['paf2gfa']['bin'] + " {input.paf} {output.gfa} --remove-all-internal"
rule paf2gfa_containment_internal:
input:
......
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