-
Notifications
You must be signed in to change notification settings - Fork 0
/
Snakefile
28 lines (22 loc) · 839 Bytes
/
Snakefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
import glob
#INPUTS
PROJECT_DIR = "/net/eichler/vol17/dutch_aspergers/nobackup/conifer_test"
BAM_SAMPLE_LIST = "samples_03-04-14.txt"
BAM_SAMPLE_BATCH_PREFIX = "sample_"
SVD_DISCARD = 9 # This parameter requires tuning
samples = []
with open(PROJECT_DIR + "/" + BAM_SAMPLE_LIST, "r") as sample_list:
for line in sample_list:
samples.append(line.split()[0])
samples = samples[1:]
#END_INPUTS
rule calcrpkm:
input: {PROJECT_DIR}"/hdf5/{samples}.h5"
shell: "./calc_rpkm.sh"
rule submit_frfast:
input: "mrfast_template_original.txt", {BAM_SAMPLE_LIST}
output: expand("%s/hdf5/{samples}.h5" % PROJECT_DIR, samples=samples)
params: frfast_batches = 5
shell: "./run_batch_frfast.sh %s" % frfast_batches
rule setup_project_env:
shell: "pushd {PROJECT_DIR}; mkdir -p hdf5 logs calls plots rpkm; popd"