diff --git a/src/Snakefiles/8-hicPipeline.sm b/src/Snakefiles/8-hicPipeline.sm index 29455983..c6c06766 100644 --- a/src/Snakefiles/8-hicPipeline.sm +++ b/src/Snakefiles/8-hicPipeline.sm @@ -181,7 +181,7 @@ echo "---Preparing rukki paths fasta" {PYTHON} {VERKKO}/scripts/get_paths_fasta.py ../{input.rukki_tsv} ../{input.unitigs_hpc} ../{input.graph_hpc} paths.hpc.fasta echo "---Running MashMap" -{params.MASHMAP} -r {params.ref} -q paths.hpc.fasta -t {threads} --pi 95.0 -s 10000 -o ../{output.path_mashmap} +{params.MASHMAP} -r {params.ref} -q paths.hpc.fasta -t {threads} -f none --pi 95.0 -s 10000 -o ../{output.path_mashmap} EOF chmod +x ./prepare_ref_mashmap.sh