Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
hem
hamlet
Commits
2b78b7d8
Commit
2b78b7d8
authored
May 04, 2018
by
bow
Browse files
Rename combine_stats to create_summary
parent
2b650477
Changes
3
Hide whitespace changes
Inline
Side-by-side
Snakefile
View file @
2b78b7d8
...
...
@@ -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",
s
tats
="{sample}/{sample}.s
tats
.json",
s
ummary
="{sample}/{sample}.s
ummary
.json",
package="{sample}/hamlet_results.{sample}.zip",
# Small variants
...
...
@@ -102,8 +102,8 @@ rule all:
for p in OUTPUTS.values()]
rule c
ombine_stats
:
"""Combines statistics across modules to a single JSON file per sample."""
rule c
reate_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/c
ombine_stats
.py"),
scr=srcdir("scripts/c
reate_summary
.py"),
params:
ver=PIPELINE_VERSION
output:
js=RUN.output(OUTPUTS["s
tats
"])
conda: srcdir("envs/c
ombine_stats
.yml")
js=RUN.output(OUTPUTS["s
ummary
"])
conda: srcdir("envs/c
reate_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:
s
tats
=RUN.output(OUTPUTS["s
tats
"]),
s
ummary
=RUN.output(OUTPUTS["s
ummary
"]),
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")),
...
...
envs/c
ombine_stats
.yml
→
envs/c
reate_summary
.yml
View file @
2b78b7d8
File moved
scripts/c
ombine_stats
.py
→
scripts/c
reate_summary
.py
View file @
2b78b7d8
File moved
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment