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pgx-main from experiment server added

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Darren Wight
2025-08-18 13:12:15 +02:00
parent ce66f54509
commit 27ba410e5b
32 changed files with 138 additions and 19 deletions
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5
pgx-main/main.nf
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@@ -773,7 +773,7 @@ process call_stars {
publishDir "$output_folder/$gene_name/alleles", mode: 'copy', overwrite: 'true'
//errorStrategy 'ignore'
errorStrategy 'ignore'
tag "${name}"
input:
@@ -787,7 +787,8 @@ process call_stars {
script:
"""
python3 ${caller_dir}/stellarpgx.py ${db}/diplo_db_debugged2.dbs ${name}_vars/${name}_core_snvs.dip ${name}_vars/${name}_full.dip ${name}_vars/${name}_gt.dip ${db}/genotypes4.dbs ${name}_gene_del/${name}_gene_del_summary.txt ${name}_gene_dup/${name}_gene_dup_summary.txt ${name}_${gene_name}_dp ${db}/haps_var_new.dbs ${db}/a_scores.dbs > ${name}_${gene_name}.alleles
python3 ${caller_dir}/stellarpgx.py ${db}/diplo_db_debugged2.dbs ${name}_vars/${name}_core_snvs.dip ${name}_vars/${name}_full.dip ${name}_vars/${name}_gt.dip ${db}/genotypes4.dbs ${name}_gene_del/${name}_gene_del_summary.txt ${name}_gene_dup/${name}_gene_dup_summary.txt ${name}_${gene_name}_dp ${db}/haps_var_new.dbs ${db}/a_scores.dbs > ${name}_${gene_name}.alleles
"""
}