-
Notifications
You must be signed in to change notification settings - Fork 0
/
config.yaml
54 lines (49 loc) · 2.6 KB
/
config.yaml
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
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
# configuration file
# BAM files - ready for input
# full path is constructed as bamloc/samples[key] at runtime, e.g.
# /prj/hIPSC_RNA_turnover_Naarmann/analysis/Krijgsveld_collaboration/mapping/161634_WTA_0h.sortdedup.bam
# bamloc directory must exists
bamloc: /prj/hIPSC_RNA_turnover_Naarmann/analysis/Krijgsveld_collaboration/mapping
samples:
161634_WTA_0h: 161634_WTA_0h.sortdedup.bam
161637_WTA_1h: 161637_WTA_1h.sortdedup.bam
161639_WTA_2h: 161639_WTA_2h.sortdedup.bam
161641_WTA_4h: 161641_WTA_4h.sortdedup.bam
161643_WTA_6h: 161643_WTA_6h.sortdedup.bam
161645_WTA_8h: 161645_WTA_8h.sortdedup.bam
161647_WTA_16h: 161647_WTA_16h.sortdedup.bam
161649_WTB_0h: 161649_WTB_0h.sortdedup.bam
161651_WTB_1h: 161651_WTB_1h.sortdedup.bam
161653_WTB_2h: 161653_WTB_2h.sortdedup.bam
161655_WTB_4h: 161655_WTB_4h.sortdedup.bam
161657_WTB_6h: 161657_WTB_6h.sortdedup.bam
161659_WTB_8h: 161659_WTB_8h.sortdedup.bam
161661_WTB_16h: 161661_WTB_16h.sortdedup.bam
161663_WTC_0h: 161663_WTC_0h.sortdedup.bam
161665_WTC_1h: 161665_WTC_1h.sortdedup.bam
161667_WTC_2h: 161667_WTC_2h.sortdedup.bam
161669_WTC_4h: 161669_WTC_4h.sortdedup.bam
161671_WTC_6h: 161671_WTC_6h.sortdedup.bam
161673_WTC_8h: 161673_WTC_8h.sortdedup.bam
161675_WTC_16h: 161675_WTC_16h.sortdedup.bam
# parent output directory - created if does not exists
# subdirectories "mapping" ("raw"), "mismatches", and "tables" (featureCounts and/or Salmon) are created
parent: /prj/hIPSC_RNA_turnover_Naarmann/analysis/Krijgsveld_collaboration/workflow
# SNPs file - ideally this file contains SNPs found on the set of all samples listed above
# NOT RECOMMENDED: comment out to run the pipeline without removing SNPs
# Default BCFtools: [--vcf] option (set vfc to True)
# we previously used the snpdata from GRAND-SLAM (default format - Location\tCoverage\tMismatches\tP value)
# If using GRAND-SLAM snpdata, see vcf: False
# snpdata: /prj/hIPSC_RNA_turnover_Naarmann/analysis/Krijgsveld_collaboration/grand-slam/results/all/all.snpdata
snpdata: /prj/hIPSC_RNA_turnover_Naarmann/analysis/Krijgsveld_collaboration/bcftools/all.snps.vcf
# program options - if unspecified uses default in splbam
base_qual: 20 # default 20
trim5p: 5 # default 0
trim3p: 5 # default 0
vcf: True # default False (for backward compatibility)
ref_base: T # default T
base_change: C # default C
# pulseR output directory - created if does not exists
# subdirectories "featureCounts" and "salmon" are created where necessary
# downstream analyses are written to subdirectories of "featureCounts" and "salmon"
pulsedir: /prj/hIPSC_RNA_turnover_Naarmann/analysis/Krijgsveld_collaboration/results