Commit b66a3926 authored by bow's avatar bow
Browse files

Add png to fsnviz output

parent be72b712
......@@ -40,9 +40,11 @@ rule plot_sf:
txt=RUN.output("{sample}/fusion/{sample}.star-fusion"),
output:
svg=RUN.output("{sample}/fusion/{sample}.star-fusion-circos/fsnviz.svg"),
png=RUN.output("{sample}/fusion/{sample}.star-fusion-circos/fsnviz.png"),
conda: srcdir("envs/plot_fusion.yml")
shell:
"PERL5LIB=\"\" fsnviz --out-dir `dirname {output.svg}` -k human.hg38 star-fusion {input.txt}"
"PERL5LIB=\"\" fsnviz --out-dir `dirname {output.svg}` --png"
" -k human.hg38 star-fusion {input.txt}"
rule plot_cp:
input:
......@@ -80,9 +82,11 @@ if do_fusioncatcher:
txt=RUN.output("{sample}/fusion/{sample}.fusioncatcher"),
output:
svg=RUN.output("{sample}/fusion/{sample}.fusioncatcher-circos/fsnviz.svg"),
png=RUN.output("{sample}/fusion/{sample}.fusioncatcher-circos/fsnviz.png"),
conda: srcdir("envs/plot_fusion.yml")
shell:
"PERL5LIB=\"\" fsnviz --out-dir `dirname {output.svg}` -k human.hg38 fusioncatcher {input.txt}"
"PERL5LIB=\"\" fsnviz --out-dir `dirname {output.svg}` --png"
" -k human.hg38 fusioncatcher {input.txt}"
rule intersect_fusions:
input:
......@@ -117,9 +121,11 @@ if do_fusioncatcher:
txt=RUN.output("{sample}/fusion/{sample}.sf-isect"),
output:
svg=RUN.output("{sample}/fusion/{sample}.sf-isect-circos/fsnviz.svg"),
png=RUN.output("{sample}/fusion/{sample}.sf-isect-circos/fsnviz.png"),
conda: srcdir("envs/plot_fusion.yml")
shell:
"PERL5LIB=\"\" fsnviz --out-dir `dirname {output.svg}` -k human.hg38 star-fusion {input.txt}"
"PERL5LIB=\"\" fsnviz --out-dir `dirname {output.svg}` --png"
" -k human.hg38 star-fusion {input.txt}"
rule combine_plots:
input:
......
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