Commit 2b78b7d8 authored by bow's avatar bow
Browse files

Rename combine_stats to create_summary

parent 2b650477
......@@ -45,7 +45,7 @@ itd_output = partial(make_pattern, dirname="itd")
OUTPUTS = dict(
# Merged FASTQs, stats, and packaged results
fqs="{sample}/{sample}-{pair}.fq.gz",
stats="{sample}/{sample}.stats.json",
summary="{sample}/{sample}.summary.json",
package="{sample}/hamlet_results.{sample}.zip",
# Small variants
......@@ -102,8 +102,8 @@ rule all:
for p in OUTPUTS.values()]
rule combine_stats:
"""Combines statistics across modules to a single JSON file per sample."""
rule create_summary:
"""Combines statistics and other info across modules to a single JSON file per sample."""
input:
seq_stats=RUN.output(OUTPUTS["seq_stats"]),
aln_stats=RUN.output(OUTPUTS["aln_stats"]),
......@@ -111,12 +111,12 @@ rule combine_stats:
insert_stats=RUN.output(OUTPUTS["insert_stats"]),
vep_stats=RUN.output(OUTPUTS["vep_stats"]),
exon_cov_stats=RUN.output(OUTPUTS["exon_cov_stats"]),
scr=srcdir("scripts/combine_stats.py"),
scr=srcdir("scripts/create_summary.py"),
params:
ver=PIPELINE_VERSION
output:
js=RUN.output(OUTPUTS["stats"])
conda: srcdir("envs/combine_stats.yml")
js=RUN.output(OUTPUTS["summary"])
conda: srcdir("envs/create_summary.yml")
shell:
"python {input.scr} {input.seq_stats} {input.aln_stats}"
" {input.rna_stats} {input.insert_stats} {input.exon_cov_stats} {input.vep_stats}"
......@@ -127,7 +127,7 @@ rule combine_stats:
rule package_results:
"""Copies essential result files into one directory and zips it."""
input:
stats=RUN.output(OUTPUTS["stats"]),
summary=RUN.output(OUTPUTS["summary"]),
smallvars_csv_all=RUN.output(OUTPUTS["smallvars_csv_all"]),
smallvars_csv_hi=RUN.output(OUTPUTS["smallvars_csv_hi"]),
smallvars_plots=RUN.output(OUTPUTS["smallvars_plots"].strip("/.done")),
......
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