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config.yml
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config.yml
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# snakeflow config file.
# 2017-03-28
# dir contains all indexes, genome sequences
genome: "/home/fangzq/genome"
# Path to an uncompressed FASTA file with all choromsome genome sequences.
# we use gencode archive, downlaod from here:
# http://www.gencodegenes.org/releases/current.html
dna: "/home/fangzq/genome/human/GRCh38.p13.genome.fa"
# Path to an uncompressed FASTA file with all transcript sequences.
# we use gencode archive, downlaod from here:
# http://www.gencodegenes.org/releases/current.html
cdna: "/home/fangzq/genome/human/GRCh38.gencode.v33.transcripts.fa"
# GTF file path
# we use gencode archive, downlaod from here:
# http://www.gencodegenes.org/releases/current.html
gtf: "/home/fangzq/genome/human/GRCh38.gencode.v33.annotation.gtf"
# RSeQC bed file
# this two files are optional, if you do not need to run RSeQC.
# Download from https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/
rseqc:
refseq: "/home/fangzq/genome/rseqc/hg38.refseq.bed"
housekeep: "/home/fangzq/genome/rseqc/hg38.HouseKeepingGenes.bed"
#trimmonatic adaptors
# adaptors:
# illumina: "/home/fangzq/github/snakeflow/adaptors/TruSeq3-PE.fa"
# Index dir
hisat2_index: "/home/fangzq/genome/hisat2Indices_hg38"
salmon_index: "/home/fangzq/genome/salmonIndices_hg38"
bowtie2_index: "/home/fangzq/genome/human/bowtie2Indices_GRCh38_noalt_as"
star_index: "/home/fangzq/genome/starIndices_hg38_100"
# Index basebame (only for hisat2)
index_prefix: "hg38"
# Full path to a folder where output files will be created.
workdir: "/data/bases/fangzq/20221015_MenYun"
# extra scripts' dir for running. e.g preDEseq.py (StringTie)
# scripts: "/home/fangzq/github/snakeflow/scripts"
# Full path to a folder that holds all of your FASTQ files
fastq_dir: "/data/bases/fangzq/20221015_MenYun/raw_fastq"
# Sequencing read length, only reqired for running rMATS or preDEseq.py.
read_length: 100
# Paired end sequencing library? True or False.
paired: True
# Stranded library ? True or False
stranded: False
# information in `samples` is used for deseq2 and rMATS
# for trimed fastq, use suffix like: _trimmed.fq.gz
read_pattern:
r1: "{sample}_1.fq.gz" # don't change {sample}
r2: "{sample}_2.fq.gz" # don't change {sample}
u: "{sample}.fastq"
# sample metadata
sample_meta: "/data/bases/fangzq/20221015_MenYun/sample.meta.txt" # PAIRED.list.txt
# ``dataframe``attribute works only if a file is given.
# each column names correspond to the samples' attributes of above.
# a sampleTable.txt look like this.
### name alias conditon treatment
## WGC096874R S74 Normal 0
## WGC096875R S75 Cancer 0
## WGC096876R S76 Normal 0
## WGC096877R S77 Cancer 0
# RNA Binding Protein list
rbps: "/home/fangzq/github/snakeflow/221RBPs.csv"
# DESeq2 cutoff
log2fc: 1
fdr: 0.01
enrichr_library: ['GO_Biological_Process_2018','GO_Cellular_Component_2018','GO_Molecular_Function_2018',
'Human_Phenotype_Ontology', 'MSigDB_Oncogenic_Signatures',
'KEGG_2016', 'KEGG_2019_Human'] # KEGG_2019_Mouse