From a5786d3a599b172926f136218adaa218527bf858 Mon Sep 17 00:00:00 2001 From: pdimens Date: Thu, 15 Aug 2024 12:42:46 -0400 Subject: [PATCH] allow secondary --- harpy/snakefiles/align_strobealign.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/harpy/snakefiles/align_strobealign.smk b/harpy/snakefiles/align_strobealign.smk index 19fc7ae98..28da53e54 100644 --- a/harpy/snakefiles/align_strobealign.smk +++ b/harpy/snakefiles/align_strobealign.smk @@ -99,7 +99,7 @@ rule align: f"{envdir}/align.yaml" shell: """ - strobealign {params.readlen} -t {threads} {params.unmapped_strobe} -C --rg-id={wildcards.sample} --rg=SM:{wildcards.sample} {params.extra} {input.genome} {input.fastq} 2> {log} | + strobealign {params.readlen} -N 2 -t {threads} {params.unmapped_strobe} -C --rg-id={wildcards.sample} --rg=SM:{wildcards.sample} {params.extra} {input.genome} {input.fastq} 2> {log} | samtools view -h {params.unmapped} -q {params.quality} > {output} """ @@ -258,7 +258,7 @@ rule workflow_summary: _ = f.write("The genome index was created using:\n") _ = f.write(f" strobealign --create-index -r {params.readlen} genome\n") _ = f.write("Sequencing were aligned with strobealign using:\n") - _ = f.write(f" strobealign --use-index {params.unmapped_strobe} -C --rg=SM:SAMPLE {params.extra} genome reads.F.fq reads.R.fq |\n") + _ = f.write(f" strobealign --use-index {params.unmapped_strobe} -N 2 -C --rg=SM:SAMPLE {params.extra} genome reads.F.fq reads.R.fq |\n") _ = f.write(f" samtools view -h {params.unmapped} -q {params.quality}\n") _ = f.write("Duplicates in the alignments were marked following:\n") _ = f.write(" samtools collate |\n")