Mercurial > repos > iuc > bcftools_gtcheck

comparison bcftools_gtcheck.xml @ 20:91c1e57d5c7f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
author iuc
date Tue, 16 Jul 2024 17:05:16 +0000
parents a29a2f40b665
children 7b4454382d39
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19:3eac729e66c9 20:91c1e57d5c7f
21 #set $genotypes_vcf = 'genotypes.vcf.gz' 21 #set $genotypes_vcf = 'genotypes.vcf.gz'
22 bgzip -c '$section.genotypes' > $genotypes_vcf && 22 bgzip -c '$section.genotypes' > $genotypes_vcf &&
23 bcftools index $genotypes_vcf && 23 bcftools index $genotypes_vcf &&
24 #elif $section.genotypes.is_of_type('bcf') 24 #elif $section.genotypes.is_of_type('bcf')
25 #set $genotypes_vcf = 'genotypes.bcf' 25 #set $genotypes_vcf = 'genotypes.bcf'
26 ln -s '$ection.genotypes' $genotypes_vcf && 26 ln -s '$section.genotypes' $genotypes_vcf &&
27 #if $section.genotypes.metadata.bcf_index: 27 #if $section.genotypes.metadata.bcf_index:
28 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi && 28 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
29 #else 29 #else
30 bcftools index $genotypes_vcf && 30 bcftools index $genotypes_vcf &&
31 #end if 31 #end if