paths fix

marbl · Jun 4, 2024 · 4814f4a · 4814f4a
1 parent 911f1f7
commit 4814f4a
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/Snakefiles/8-hicPipeline.sm b/src/Snakefiles/8-hicPipeline.sm
@@ -178,10 +178,10 @@ cat > ./prepare_ref_mashmap.sh <<EOF
 #!/bin/sh
 set -e
 echo "---Preparing rukki paths fasta"
-{PYTHON} {VERKKO}/scripts/get_paths_fasta.py ../{input.rukki_tsv} ../{input.unitigs_hpc} ../{input.graph_hpc} paths.hpc.fasta
+{PYTHON} {VERKKO}/scripts/get_paths_fasta.py ../{input.rukki_tsv} ../{input.unitigs_hpc} ../{input.graph_hpc} ../8-hicPipeline/paths.hpc.fasta
 
 echo "---Running MashMap"
-{params.MASHMAP} -r {params.ref}  -q paths.hpc.fasta -t {threads}  -f none --pi 95.0 -s 10000 -o ../{output.path_mashmap}
+{params.MASHMAP} -r ../{params.ref}  -q ../8-hicPipeline/paths.hpc.fasta -t {threads}  -f none --pi 95.0 -s 10000 -o ../{output.path_mashmap}
 EOF
 
 chmod +x ./prepare_ref_mashmap.sh