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#!/usr/bin/env python | ||
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import getpass | ||
import os | ||
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# Required user input: | ||
# 1) Which fusion prediction tools should be executed (tools) | ||
# 2) Which post-processing steps should be executed (fd_tools) | ||
# 3) Which reference data shall be used (ref_trans_version & ref_genome_build) | ||
# 4) To whom shall slurm mails be sent to (receiver) | ||
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__version__ = "1.3.1" | ||
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pipeline_name = "EasyFuse" | ||
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#tools=Readfilter,Mapsplice,Fusioncatcher,Star,Starfusion,Infusion,Fetchdata,Summary | ||
tools = ("QC", | ||
"Readfilter", | ||
"Fusioncatcher", | ||
"Star", | ||
"Starfusion", | ||
"Infusion", | ||
"Mapsplice", | ||
"Soapfuse", | ||
"Fetchdata", | ||
"Summary") | ||
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fusiontools = ("Fusioncatcher", | ||
"Starfusion", | ||
"Infusion", | ||
"Mapsplice", | ||
"Soapfuse") | ||
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#fd_tools=Fusiongrep,Contextseq,Starindex,Staralign,Bamindex,Requantify | ||
fd_tools = ("Fusiongrep", | ||
"Contextseq", | ||
"Starindex", | ||
"ReadFilter2", | ||
"ReadFilter2b", | ||
"StaralignBest", | ||
"BamindexBest", | ||
"RequantifyBest") | ||
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sender = "[email protected]" | ||
receiver = "[email protected]" | ||
min_read_len_perc = 0.75 | ||
max_dist_proper_pair = 200000 | ||
cis_near_distance = 1000000 | ||
model_pred_threshold = 0.75 | ||
tsl_filter = "4,5,NA" | ||
requant_mode = ["best"] | ||
context_seq_len = 400 | ||
ref_genome_build = "hg38" | ||
ref_trans_version = "ensembl" | ||
queueing_system = "slurm" | ||
time_limit = "30-00:00:0" | ||
partition = "Compute" | ||
user = getpass.getuser() | ||
module_dir = os.path.dirname(os.path.realpath(__file__)) | ||
#logfile=/data/urla_progs/TronData/ngs_pipelines/easyfuse/fusion.log | ||
#fusion_db=/data/urla_progs/TronData/ngs_pipelines/easyfuse/fusion.db | ||
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# Define ressource usage (cpu (number of threads), mem (ram in Gb)): | ||
resources = { | ||
"qc": { | ||
"cpu": 6, | ||
"mem": 10 | ||
}, | ||
"readfilter": { | ||
"cpu": 6, | ||
"mem": 50 | ||
}, | ||
"star": { | ||
"cpu": 6, | ||
"mem": 40 | ||
}, | ||
"kallisto": { | ||
"cpu": 6, | ||
"mem": 10 | ||
}, | ||
"mapsplice": { | ||
"cpu": 6, | ||
"mem": 30 | ||
}, | ||
"fusioncatcher": { | ||
"cpu": 6, | ||
"mem": 30 | ||
}, | ||
"starfusion": { | ||
"cpu": 6, | ||
"mem": 30 | ||
}, | ||
"starchip": { | ||
"cpu": 12, | ||
"mem": 30 | ||
}, | ||
"infusion": { | ||
"cpu": 6, | ||
"mem": 30 | ||
}, | ||
"soapfuse": { | ||
"cpu": 6, | ||
"mem": 20 | ||
}, | ||
"classification": { | ||
"cpu": 1, | ||
"mem": 16 | ||
}, | ||
"fetchdata": { | ||
"cpu": 12, | ||
"mem": 50 | ||
}, | ||
"summary": { | ||
"cpu": 1, | ||
"mem": 16 | ||
} | ||
} | ||
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# execution command for individual programs (what you write here should be identical to what is typed in the console) | ||
commands = { | ||
# for qc | ||
"fastqc": "/path/to/fastqc_bin", | ||
"skewer": "/path/to/skewer_bin", | ||
# for processing | ||
"mapsplice": "/path/to/mapsplice.py", | ||
"fusioncatcher": "/path/to/fusioncatcher_bin", | ||
"starfusion": "/path/to/starfusion_bin", | ||
"infusion": "/path/to/infusion_bin", | ||
"soapfuse": "/path/to/SOAPfuse-RUN.pl", | ||
# for processing and fetch data | ||
"star": "/path/to/star_bin", | ||
"samtools": "/path/to/samtools_bin" | ||
# for liftover | ||
#"crossmap": "test" | ||
} | ||
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# full path to reference files | ||
references = { | ||
# wget http://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz | ||
"genome_fasta": "/path/to/Homo_sapiens.GRCh38.dna.primary_assembly.fa", | ||
"genome_fastadir": "/projects/data/human/ensembl/GRCh38.86/fasta", | ||
"genome_sizes": "/projects/data/human/ensembl/GRCh38.86/STAR_idx/chrNameLength.txt", | ||
# wget http://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz | ||
"genes_fasta": "/projects/data/human/ensembl/GRCh38.86/Homo_sapiens.GRCh38.cdna.all.fa", | ||
# wget http://ftp.ensembl.org/pub/release-86/gtf/homo_sapiens/Homo_sapiens.GRCh38.86.chr.gtf.gz | ||
"genes_gtf": "/path/to/Homo_sapiens.GRCh38.86.gtf", | ||
"genes_adb": "/projects/data/human/ensembl/GRCh38.86/Homo_sapiens.GRCh38.86.gff3.db", | ||
"genes_tsl": "/projects/data/human/ensembl/GRCh38.86/Homo_sapiens.GRCh38.86.gtf.tsl" | ||
} | ||
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# full path to program indices | ||
indices = { | ||
"star": "/projects/data/human/ensembl/GRCh38.86/STAR_idx/", | ||
"bowtie": "/projects/data/human/ensembl/GRCh38.86/bowtie_index/hg38", | ||
"starfusion": "/projects/data/human/ensembl/GRCh38.86/starfusion_index/", | ||
"fusioncatcher": "/projects/data/human/ensembl/GRCh38.86/fusioncatcher_index/" | ||
} | ||
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# full path to program specific config files (these are just general files which need no user modification) | ||
other_files = { | ||
"infusion_cfg": "/projects/data/human/ensembl/GRCh38.86/infusion_index/infusion.cfg", | ||
"soapfuse_cfg": "/code/SOAPfuse/1.27/config/config_h86.txt", | ||
"soapfuse_cfg_mm10": "/code/SOAPfuse/1.27/config/config_m95.txt", | ||
"easyfuse_model": os.path.join(module_dir, "data", "model", "Fusion_modeling_IVAC_BNT_v16.model.requant_and_boundary_org.randomForest.rds") | ||
} |
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