From 145cc696be3174c87287bd393b9ef2be8fc29433 Mon Sep 17 00:00:00 2001 From: Abhinav Sharma Date: Thu, 22 Oct 2020 20:11:49 +0530 Subject: [PATCH] got haplotype_caller.nf working with mtb genomes --- modules/gatk/haplotype_caller/haplotype_caller.nf | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/modules/gatk/haplotype_caller/haplotype_caller.nf b/modules/gatk/haplotype_caller/haplotype_caller.nf index 66563a5..6c6b938 100644 --- a/modules/gatk/haplotype_caller/haplotype_caller.nf +++ b/modules/gatk/haplotype_caller/haplotype_caller.nf @@ -18,8 +18,7 @@ process GATK_HAPLOTYPE_CALLER { input: tuple path(ref_fasta), path(ref_fasta_index) path(ref_dict) - // FIXME - path(input_bam) + tuple path(input_bam), path(input_bam_index) path(interval_list) @@ -61,7 +60,7 @@ workflow test { ref_dict_ch = Channel.value(Paths.get("${baseDir}/test_data/Homo_sapiens_assembly38.dict")) - input_bam_ch = Channel.fromPath("${baseDir}/test_data/*bam*").collect() + input_bam_ch = Channel.fromPath("${baseDir}/test_data/*bam*").toSortedList().flatten().collate(2) interval_list_ch = Channel.value(Paths.get("${baseDir}/test_data/test-intervals.hg38.list"))