## Metasheet location. If you change the name of your metasheet or its location from where you are running VIPER from, you must change it here.
metasheet: metasheet.csv
ref: ref.yaml

#possible values are, true and false
stranded: true
# if stranded true, library_type is a required argument
# Possible values are [ff-firststrand, ff-secondstrand, ff-unstranded, fr-firststrand, fr-secondstrand, fr-unstranded (default), transfrags]
library_type: fr-firststrand

analysis_token: paper_run

###PARAMS

## Sample-Sample Heatmap params
RPKM_threshold: 1.0
min_num_samples_expressing_at_threshold: 2

filter_mirna: true
#filter_mirna: false

numgenes_plots: 1000

num_kmeans_clust: 4,3,0

#Turn on the following if you want a genome wide snp scan in addition to chr6 scan
snp_scan_genome: true

# If this flag is on, you must have a metasheet column called batch with at least 2 samples per batch                                           
batch_effect_removal: false

## Value that determines which genes are significant and should be considered for GOterm analysis
goterm_adjpval_cutoff: 0.05
## Number of GOterms to plot out
numgoterms: 20
## Number of KEGG pathways to plot out
numkeggpathways: 5

#Uncomment the following line to perform TIMER (immunology) analysis. refer to 
#README.md
cancer_type: 'sarc'

#Uncomment the following if you want to perform a scan of viral dna on your samples
# possible value are ["true","false"]
virus_dna_scan: true

#Uncomment the following line to perform a TRUST (cdr3) analysis.  refer to README.md
cdr3_analysis: true

#Path to gene set enrichment db
gsea_db: viper/static/gsea/msigdb.v6.1.symbols.gmt

# the_samples:
# sample names, e.g. "MY_Sample01" "MY_Sample02" can be any abitrary string
# HOWEVER, these names must match what is in metasheet.csv
#
# FOR each sample, define the path to the raw data, either fastq.gz or bam
# IF it is a paired-end sample, use a second line 
# (e.g. see MY_Sample01--remove the hashtag at the beginning)
#
# KEY NOTE: it is recommended that you make a symbolic link to your raw files
# e.g. $ ln -s /path/to/my/raw/data ./data
### SAMPLES

samples:
    TA12:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150926-TA12-20150414-IDX10-PR2340_S1_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150926-TA12-20150414-IDX10-PR2340_S1_R2_001.fastq.gz
    BA47:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151008-BA47-20150429-IDX27-PR2354_S2_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151008-BA47-20150429-IDX27-PR2354_S2_R2_001.fastq.gz
    BA03:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150925-BA03-20150414-IDX2-PR2339_S2_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150925-BA03-20150414-IDX2-PR2339_S2_R2_001.fastq.gz
    BA43:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151008-BA43-20150429-IDX13-PR2353_S3_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151008-BA43-20150429-IDX13-PR2353_S3_R2_001.fastq.gz
    BA05:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150925-BA05-20150414-IDX4-PR2339_S4_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150925-BA05-20150414-IDX4-PR2339_S4_R2_001.fastq.gz
    BA19:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151002-BA19-20150429-IDX13-PR2351_S5_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151002-BA19-20150429-IDX13-PR2351_S5_R2_001.fastq.gz
    BA61:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151008-BA61-20150429-IDX3-PR2354_S5_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151008-BA61-20150429-IDX3-PR2354_S5_R2_001.fastq.gz
    TA06:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150928-TA06-20150414-IDX22-PR2349_S5_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150928-TA06-20150414-IDX22-PR2349_S5_R2_001.fastq.gz
    TA18:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151001-TA18-20150429-IDX5-PR2350_S5_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151001-TA18-20150429-IDX5-PR2350_S5_R2_001.fastq.gz
    BP03:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151001-BP03-20150429-IDX20-PR2350_S6_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151001-BP03-20150429-IDX20-PR2350_S6_R2_001.fastq.gz
    BP01:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150926-BP01-20150414-IDX20-PR2340_S7_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150926-BP01-20150414-IDX20-PR2340_S7_R2_001.fastq.gz
    BA09:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150925-BA09-20150414-IDX8-PR2339_S8_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150925-BA09-20150414-IDX8-PR2339_S8_R2_001.fastq.gz
    BP05:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151001-BP05-20150429-IDX22-PR2350_S8_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20151001-BP05-20150429-IDX22-PR2350_S8_R2_001.fastq.gz
    BA14:
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150925-BA14-20150414-IDX13-PR2339_S12_R1_001.fastq.gz
        - /mnt/cfce-stor1/data/port/20160624_mbcf/160211_Weinstock_ExampleData_VIPER/data/20150925-BA14-20150414-IDX13-PR2339_S12_R2_001.fastq.gz
