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mustard_chr6.yaml
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mustard_chr6.yaml
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## Copyright 2016 UCSC Computational Genomics Lab
## Original contributor: Arjun Arkal Rao
##
## Licensed under the Apache License, Version 2.0 (the "License");
## you may not use this file except in compliance with the License.
## You may obtain a copy of the License at
##
## http://www.apache.org/licenses/LICENSE-2.0
##
## Unless required by applicable law or agreed to in writing, software
## distributed under the License is distributed on an "AS IS" BASIS,
## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
## See the License for the specific language governing permissions and
## limitations under the License.
####################################################################################################
####################################################################################################
## This is the input parameter file for the precision immuno pipeline. The parameters for each of
## the tools is provided here. The file is written in the YAML format. A nice description of the
## format can be found at http://docs.ansible.com/ansible/YAMLSyntax.html
##
## You can add comments anywhere in this file by prefixing it with a '#'
##
## Unless otherwise mentioned, all fields must be filled.
##
####################################################################################################
####################################################################################################
# Any number of patients/samples can be listed here
patients:
CHR6:
tumor_dna_fastq_1: /scratch/drkthomp/chr6_only/tumor_chr6_1.fastq
tumor_dna_fastq_2: /scratch/drkthomp/chr6_only/tumor_chr6_2.fastq
normal_dna_fastq_1: /scratch/drkthomp/chr6_only/normal_chr6_1.fastq
normal_dna_fastq_2: /scratch/drkthomp/chr6_only/normal_chr6_2.fastq
tumor_rna_fastq_1: /scratch/drkthomp/chr6_only/chr6_1.fastq
tumor_rna_fastq_2: /scratch/drkthomp/chr6_only/chr6_2.fastq
#tumor_rna_bam: /scratch/drkthomp/rna_genome_sortedmd.bam
#mutation_vcf: /scratch/drkthomp/chr6_only/variants_chr6.vcf
#hla_haplotype_files: /scratch/drkthomp/haplotypes.tar.gz
tumor_type: 'SKCM'
# These are options that are used by most tools
Universal_Options:
dockerhub: aarjunrao
java_Xmx: 12G
reference_build: GRCh38 # Acceptable options are hg38, hg38, GRCh37, GRCh38
# sse_key: /path/to/master.key # Path to the AWS master key. Required if using AWS else optional
# sse_key_is_master: True # True or False. Required if using AWS else optional
# gdc_download_token: /path/to/token.txt # Path to the user's GDC download token.
storage_location: Local # Local or aws:<bucket_name> for where the output must go
#storage_location: aws:protect-run-xyz
output_folder: /scratch/drkthomp/results # Path to where the output must go.
#mail_to: [email protected] # Email patients:
#TEST:
# tumor_dna_fastq_1: /home/drkthomp/e/treehouse/gms/hcc1395_1tenth_percent/sort/gerald_D1VCPACXX_1_R1.fastq
# tumor_dna_fastq_2: /home/drkthomp/e/treehouse/gms/hcc1395_1tenth_percent/sort/gerald_D1VCPACXX_1_R2.fastq
# normal_dna_fastq_1: /home/drkthomp/e/treehouse/gms/hcc1395_1tenth_percent/sort/gerald_D1VCPACXX_6_R1.fastq
# normal_dna_fastq_2: /home/drkthomp/e/treehouse/gms/hcc1395_1tenth_percent/sort/gerald_D1VCPACXX_6_R2.fastq
# tumor_rna_fastq_1: /home/drkthomp/e/treehouse/gms/hcc1395_1tenth_percent/sort/gerald_C1TD1ACXX_8_ACAGTG_R1.fastq
# tumor_rna_fastq_2: /home/drkthomp/e/treehouse/gms/hcc1395_1tenth_percent/sort/gerald_C1TD1ACXX_8_ACAGTG_R2.fastq
# tumor_type: 'SKCM'
# for sending success report.
# These options are for each module. You probably don't need to change any of this!
alignment:
cutadapt:
a: AGATCGGAAGAG
A: AGATCGGAAGAG
# version: 1.9.1
star:
type: star # use starlong if your reads are > 150bp
index: /scratch/drkthomp/protect-index/star_with_fusion_100bp_readlen_indexes.tar.gz # Use star_without if you set star_fusion = False
# version: 2.5.2b
bwa:
index: /scratch/drkthomp/protect-index/bwa_index.tar.gz
# version: 0.7.9a
post:
samtools:
# version: 1.2
picard:
# version: 1.135
expression_estimation:
rsem:
index: /scratch/drkthomp/protect-index/rsem_index.tar.gz
# version: 1.2.0
mutation_calling:
indexes:
chromosomes: canonical_chr, chrM
genome_fasta: /scratch/drkthomp/protect-index/hg38.fa.tar.gz
genome_fai: /scratch/drkthomp/protect-index/hg38.fa.fai.tar.gz
genome_dict: /scratch/drkthomp/protect-index/hg38.dict.tar.gz
cosmic_vcf: /scratch/drkthomp/protect-index/CosmicCodingMuts.vcf.tar.gz
cosmic_idx: /scratch/drkthomp/protect-index/CosmicCodingMuts.vcf.idx.tar.gz
dbsnp_vcf: /scratch/drkthomp/protect-index/dbsnp_coding.vcf.gz
dbsnp_idx: /scratch/drkthomp/protect-index/dbsnp_coding.vcf.idx.tar.gz
dbsnp_tbi: /scratch/drkthomp/protect-index/dbsnp_coding.vcf.gz.tbi
mutect:
java_Xmx: 2G
# version: 1.1.7
muse:
# version: 1.0rc_submission_b391201
radia:
cosmic_beds: /scratch/drkthomp/protect-index/radia_cosmic.tar.gz
dbsnp_beds: /scratch/drkthomp/protect-index/radia_dbsnp.tar.gz
retrogene_beds: /scratch/drkthomp/protect-index/radia_retrogenes.tar.gz
pseudogene_beds: /scratch/drkthomp/protect-index/radia_pseudogenes.tar.gz
gencode_beds: /scratch/drkthomp/protect-index/radia_gencode.tar.gz
# version: 398366ef07b5911d8082ed61cbf03d487a41f286
somaticsniper:
# version: 1.0.4
samtools:
# version: 0.1.8
bam_readcount:
# version: 0.7.4
star_fusion:
#run: True
#version: 1.0.0
fusion_inspector:
#run_trinity: True
#version: 1.0.1
strelka:
# version: 1.0.15
config_file: /scratch/drkthomp/protect-index/strelka_bwa_WXS_config.ini.tar.gz
mutation_annotation:
snpeff:
index: /scratch/drkthomp/protect-index/snpeff_index.tar.gz
# version: 3.6
java_Xmx: 20G
mutation_translation:
transgene:
gencode_peptide_fasta : /scratch/drkthomp/protect-index/gencode.v25.pc_translations_NOPARY.fa.tar.gz
gencode_transcript_fasta : /scratch/drkthomp/protect-index/gencode.v25.pc_transcripts_NOPARY.fa.tar.gz
gencode_annotation_gtf : /scratch/drkthomp/protect-index/gencode.v25.annotation_NOPARY.gtf.tar.gz
genome_fasta : /scratch/drkthomp/protect-index/hg38.fa.tar.gz
# version: 2.2.2
haplotyping:
phlat:
index: /scratch/drkthomp/protect-index/phlat_index.tar.gz
# version: 1.0
mhc_peptide_binding:
mhci:
method_file: /scratch/drkthomp/protect-index/mhci_restrictions.json.tar.gz
pred: IEDB_recommended
# version: 2.13
mhcii:
method_file: /scratch/drkthomp/protect-index/mhcii_restrictions.json.tar.gz
pred: IEDB_recommended
# version: 2.13
netmhciipan:
# version: 3.1
prediction_ranking:
rankboost:
mhci_args:
npa: 0.0
nph: 0.0
nMHC: 0.32
TPM: 0.0
overlap: 0.68
tndelta: 0.0
mhcii_args:
npa: 0.2
nph: 0.2
nMHC: 0.2
TPM: 0.2
tndelta: 0.2
# version: 2.0.3
reports:
mhc_pathways_file: /scratch/drkthomp/protect-index/mhc_pathways.tsv.tar.gz
itx_resistance_file: /scratch/drkthomp/protect-index/itx_resistance.tsv.tar.gz
immune_resistance_pathways_file: /scratch/drkthomp/protect-index/immune_resistance_pathways.json.tar.gz
car_t_targets_file: /scratch/drkthomp/protect-index/car_t_targets.tsv.tar.gz