From ce7b856ddfdf97c4c40f25763ca65e5e18c4c1e8 Mon Sep 17 00:00:00 2001 From: ASLeonard Date: Thu, 16 Nov 2023 17:04:59 +0100 Subject: [PATCH] use pangenie scripts --- snakepit/pangenie_panel.smk | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/snakepit/pangenie_panel.smk b/snakepit/pangenie_panel.smk index 8c2bca0..5412933 100644 --- a/snakepit/pangenie_panel.smk +++ b/snakepit/pangenie_panel.smk @@ -21,7 +21,6 @@ configfile: "config.json" samples = config['assemblies'].keys() samples_parents = [s for s in samples if not s in config['trios']] scripts = config['scripts'] -mscripts = config['mscripts'] outdir = config['outdir'] chromosomes = list(map(str,range(1,30))) #[str(i) for i in range(1,23)] + [config['reference']['prefix'] + 'X', config['reference']['prefix'] + 'Y'] frac_missing = config.get('frac_missing',0.2) # skip positions with more than this fraction of missing alleles @@ -241,7 +240,7 @@ rule combine_haplotypes: mem_mb=10000, walltime = '24:00' shell: - 'python3 {mscripts}/merge_vcfs.py combine_columns -samples {input.samples} -vcf {input.haps} > {output}' + 'python3 {scripts}/merge_vcfs.py combine_columns -samples {input.samples} -vcf {input.haps} > {output}' ################################################################# @@ -287,7 +286,7 @@ rule check_mendelian_consistency: walltime = '24:00' shell: """ - python3 {mscripts}/mendelian-consistency.py filter -vcf {input.vcf} -samples {input.samples} -ped {input.ped} -o {output.tsv} > {output.vcf} + python3 {scripts}/mendelian-consistency.py filter -vcf {input.vcf} -samples {input.samples} -ped {input.ped} -o {output.tsv} > {output.vcf} """ rule merge_haplotypes: @@ -304,7 +303,7 @@ rule merge_haplotypes: walltime = '4:00' shell: """ - python3 {mscripts}/merge_vcfs.py merge -vcf {input.vcf} -r {input.reference} -ploidy 2 -chromosomes {wildcards.chr} -max_edit_distance 0.02 > {output.tmp} + python3 {scripts}/merge_vcfs.py merge -vcf {input.vcf} -r {input.reference} -ploidy 2 -chromosomes {wildcards.chr} -max_edit_distance 0.02 > {output.tmp} """ #############################################