From 9302efa593249bc48bd8ff86eb90d90164a1f774 Mon Sep 17 00:00:00 2001 From: Dmitry Antipov Date: Mon, 3 Jun 2024 09:01:03 -0400 Subject: [PATCH] snakemake fix --- src/Snakefiles/8-hicPipeline.sm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/Snakefiles/8-hicPipeline.sm b/src/Snakefiles/8-hicPipeline.sm index d051666f..a9874702 100644 --- a/src/Snakefiles/8-hicPipeline.sm +++ b/src/Snakefiles/8-hicPipeline.sm @@ -107,7 +107,7 @@ echo "---Running MashMap" {params.MASHMAP} -r ../{input.unitigs_hpc} -q ../{input.unitigs_hpc} -t {threads} -f none --pi {params.MASHMAP_DIV} -s 10000 -o mashmap.out cat mashmap.out |awk '{{if (\$4-\$3 > 100000 && \$1 != \$6) print \$1"\\t"\$6"\\t"\$4-\$3}}'|sort |uniq > ../{output.unitigs_matches} {params.MASHMAP} -r ../{input.unitigs} -q ../{input.unitigs} -t {threads} -f none --pi {params.MASHMAP_DIV} -s 10000 -o unitigs_nonhpc.mashmap -awk '$11 >= 50000' unitigs_nonhpc.mashmap > ../{output.unitigs_nohpc50} +awk '\$11 >= 50000' unitigs_nonhpc.mashmap > ../{output.unitigs_nohpc50} EOF chmod +x ./run_mashmap.sh