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Beatrice Tan
CNAprioritization
Commits
3e2c380f
Commit
3e2c380f
authored
Feb 02, 2018
by
Tan
Browse files
Updated run rule for running different sample sizes with GISTIC2.
parent
0c50f100
Changes
4
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Snakefile
View file @
3e2c380f
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@@ -42,7 +42,7 @@ onerror:
rule all:
"""Define desired output from pipeline."""
input:
os.path.join(config["gisticdir"], "gistic2")
"Samplesize/Report.txt"
#"Reports/Results.html"
...
...
config.yaml
View file @
3e2c380f
...
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@@ -34,6 +34,6 @@ settings_gistic: "-ta 0.1
-conf
0.99"
#Settings for sample size differences
#
sizes: [30, 40, 50, 60, 70, 80, 90]
sizes
:
[
30
,
40
]
sizes
:
[
20
,
30
,
40
,
50
,
60
,
70
,
80
,
90
]
#
sizes: [30, 40]
repeats
:
[
1
,
2
,
3
,
4
,
5
,
6
,
7
,
8
,
9
,
10
,
11
,
12
,
13
,
14
,
15
,
16
,
17
,
18
,
19
,
20
]
rules/SampleSizes.smk
View file @
3e2c380f
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@@ -18,9 +18,9 @@ rule run_gistic_subsets:
seg="Samplesize/Input/Size{rand_nr}.Rep{rep_nr}.txt"
output:
"Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt"
"Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed"
params:
cnv="",
gistic_directory=config["gisticdir"],
ref=config["reference"],
ref_file="",
extra=config["settings_gistic"]
...
...
@@ -50,7 +50,7 @@ rule run_rubic_subsets:
rule report_sizes:
"""Report the difference when using different sample sizes."""
input:
#
gistic=expand("Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
gistic=expand("Samplesize/GISTIC/Size{rand_nr}.Rep{rep_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
rubic_gains=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/gains.txt", rand_nr=config["sizes"], rep_nr=config["repeats"]),
rubic_losses=expand("Samplesize/RUBIC/Size{rand_nr}.Rep{rep_nr}/losses.txt", rand_nr=config["sizes"], rep_nr=config["repeats"])
output:
...
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run_pipeline_cluster.sh
View file @
3e2c380f
...
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@@ -18,7 +18,7 @@ snakemake -p \
--configfile
config.yaml
\
--snakefile
Snakefile
\
--latency-wait
90
\
--jobs
1
\
--jobs
3
\
--max-jobs-per-second
10
\
--restart-times
3
\
--use-conda
\
...
...
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