snakemake fix

marbl · Jun 3, 2024 · 9302efa · 9302efa
1 parent b789ca8
commit 9302efa
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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