Commit cce7010e authored by van den Berg's avatar van den Berg
Browse files

Increase the maximum number of junction reads

Fusioncatcher crashes if the maximum number of junction reads is
exceeded. This commit adds a parameter to the fusioncatcher rule to
make this configurable, and also increases the default limit from 100000
to 150000.
parent 4cdbffa4
Pipeline #5710 failed with stages
......@@ -94,7 +94,8 @@ rule fusioncatcher:
fq1="{sample}/{sample}-R1.raw.fq.gz",
fq2="{sample}/{sample}-R2.raw.fq.gz",
params:
data=settings["fusioncatcher_data"]
data=settings["fusioncatcher_data"],
max_junctions=1500000
output:
txt="{sample}/fusion/fusioncatcher/final-list_candidate-fusion-genes.txt"
threads: 8
......@@ -102,7 +103,7 @@ rule fusioncatcher:
shell:
" dir=`dirname {output.txt}` "
" && fusioncatcher.py --threads {threads} -i {input.fq1},{input.fq2} -o ${{dir}}"
" --data {params.data} || test -f {output.txt}"
" --data {params.data} --limitSjdbInsertNsj {params.max_junctions} || test -f {output.txt}"
rule fusioncatcher_cp:
input:
......
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