From 9c716eebd2c193a079ec7f44dff5381907044937 Mon Sep 17 00:00:00 2001 From: "katarzyna.otylia.sikora@gmail.com" Date: Tue, 7 Jan 2025 13:29:10 +0100 Subject: [PATCH] sorted --- snakePipes/shared/rules/whatshap.snakefile | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/snakePipes/shared/rules/whatshap.snakefile b/snakePipes/shared/rules/whatshap.snakefile index 614f0ff54..261bb0945 100644 --- a/snakePipes/shared/rules/whatshap.snakefile +++ b/snakePipes/shared/rules/whatshap.snakefile @@ -5,7 +5,7 @@ rule whatshap_haplotag: bam = "filtered_bam/{sample}.filtered.bam", bai = "filtered_bam/{sample}.filtered.bam.bai" output: - hbam = "allelic_bams/{sample}.filtered.allele_flagged.bam", + hbam = "allelic_bams/{sample}.filtered.allele_flagged.sorted.bam", hlist = "allelic_bams/{sample}.filtered_haplotype_list.tsv" benchmark: "allelic_bams/.benchmark/whatshap_haplotag.{sample}.benchmark" @@ -17,12 +17,12 @@ rule whatshap_haplotag: rule whatshap_split: input: - hbam = "allelic_bams/{sample}.filtered.allele_flagged.bam", + hbam = "allelic_bams/{sample}.filtered.allele_flagged.sorted.bam", hlist = "allelic_bams/{sample}.filtered_haplotype_list.tsv" output: - h1bam = "allelic_bams/{sample}.filtered.genome1.bam", - h2bam = "allelic_bams/{sample}.filtered.genome2.bam", - unbam = "allelic_bams/{sample}.filtered.unassigned.bam" + h1bam = "allelic_bams/{sample}.filtered.genome1.sorted.bam", + h2bam = "allelic_bams/{sample}.filtered.genome2.sorted.bam", + unbam = "allelic_bams/{sample}.filtered.unassigned.sorted.bam" benchmark: "allelic_bams/.benchmark/whatshap_split.{sample}.benchmark" conda: CONDA_WHATSHAP_ENV