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hem
hamlet
Commits
60d88d49
Commit
60d88d49
authored
May 22, 2019
by
van den Berg
Browse files
Rename report output since it is a reserved key
parent
e44137f1
Changes
1
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60d88d49
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@@ -49,7 +49,7 @@ OUTPUTS = dict(
# Merged FASTQs, stats, and packaged results
fqs="{sample}/{sample}-{pair}.fq.gz",
summary="{sample}/{sample}.summary.json",
report="{sample}/hamlet_report.{sample}.pdf",
report
je
="{sample}/hamlet_report.{sample}.pdf",
package="{sample}/hamlet_results.{sample}.zip",
# Small variants
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@@ -157,7 +157,7 @@ rule generate_report:
toc=srcdir("report/assets/toc.xsl"),
scr=srcdir("scripts/generate_report.py"),
output:
pdf=RUN.output(OUTPUTS["report"]),
pdf=RUN.output(OUTPUTS["report
je
"]),
conda: srcdir("envs/create_report.yml")
shell:
"python {input.scr}"
...
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@@ -184,7 +184,7 @@ rule package_results:
kmt_csv=RUN.output(OUTPUTS["kmt2a_csv"]),
kmt_bg_csv=RUN.output(OUTPUTS["kmt2a_bg_csv"]),
kmt_png=RUN.output(OUTPUTS["kmt2a_png"]),
report=RUN.output(OUTPUTS["report"]),
report
je
=RUN.output(OUTPUTS["report
je
"]),
output:
pkg=RUN.output(OUTPUTS["package"]),
params:
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