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snakemake_config.yaml
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# Resource allocation
create_star_index_threads: 4
create_star_index_mem_gb: 40
create_star_index_time_hr: 12
iris_append_sjc_mem_gb: 8
iris_append_sjc_time_hr: 24
# TODO 16 threads hardcoded in iris process_rnaseq
iris_cuff_task_threads: 8
iris_cuff_task_mem_gb: 8
iris_cuff_task_time_hr: 12
iris_epitope_post_mem_gb: 8
iris_epitope_post_time_hr: 12
iris_exp_matrix_mem_gb: 8
iris_exp_matrix_time_hr: 12
iris_extract_sjc_task_mem_gb: 8
iris_extract_sjc_task_time_hr: 12
iris_format_mem_gb: 8
iris_format_time_hr: 12
# TODO seq2HLA defaults to 6 threads since IRIS does not supply the -p argument
iris_hla_task_threads: 6
iris_hla_task_mem_gb: 8
iris_hla_task_time_hr: 12
iris_parse_hla_mem_gb: 8
iris_parse_hla_time_hr: 12
iris_predict_mem_gb: 8
iris_predict_time_hr: 12
iris_predict_task_mem_gb: 8
iris_predict_task_time_hr: 12
# TODO 8 hardcoded in makesubsh_rmats
iris_rmats_task_threads: 8
iris_rmats_task_mem_gb: 8
iris_rmats_task_time_hr: 12
# TODO 8 hardcoded in makesubsh_rmatspost
iris_rmatspost_task_threads: 8
iris_rmatspost_task_mem_gb: 8
iris_rmatspost_task_time_hr: 12
iris_screen_mem_gb: 8
iris_screen_time_hr: 12
iris_screen_sjc_mem_gb: 8
iris_screen_sjc_time_hr: 12
iris_sjc_matrix_mem_gb: 8
iris_sjc_matrix_time_hr: 12
# TODO 6 threads hardcoded in iris process_rnaseq
iris_star_task_threads: 6
iris_star_task_mem_gb: 40
iris_star_task_time_hr: 12
iris_visual_summary_mem_gb: 8
iris_visual_summary_time_hr: 12
# Command options
run_core_modules: true
# run_all_modules toggles which rules can be run by
# conditionally adding UNSATISFIABLE_INPUT to certain rules.
run_all_modules: false
should_run_sjc_steps: true
star_sjdb_overhang: 100
run_name: 'NEPC_test' # used to name output files
splice_event_type: 'SE' # one of [SE, RI,A3SS, A5SS]
comparison_mode: 'group' # group or individual
stat_test_type: 'parametric' # parametric or nonparametric
use_ratio: false
tissue_matched_normal_psi_p_value_cutoff: ''
tissue_matched_normal_sjc_p_value_cutoff: ''
tissue_matched_normal_delta_psi_p_value_cutoff: ''
tissue_matched_normal_fold_change_cutoff: ''
tissue_matched_normal_group_count_cutoff: ''
tissue_matched_normal_reference_group_names: ''
tumor_psi_p_value_cutoff: ''
tumor_sjc_p_value_cutoff: ''
tumor_delta_psi_p_value_cutoff: ''
tumor_fold_change_cutoff: ''
tumor_group_count_cutoff: ''
tumor_reference_group_names: ''
normal_psi_p_value_cutoff: '0.01'
normal_sjc_p_value_cutoff: '0.000001'
normal_delta_psi_p_value_cutoff: '0.05'
normal_fold_change_cutoff: '1'
normal_group_count_cutoff: '8'
normal_reference_group_names: 'GTEx_Heart,GTEx_Blood,GTEx_Lung,GTEx_Liver,GTEx_Brain,GTEx_Nerve,GTEx_Muscle,GTEx_Spleen,GTEx_Thyroid,GTEx_Skin,GTEx_Kidney'
# Input files
# sample_fastqs are not needed when just running the core modules
# sample_fastqs:
# sample_name_1:
# - '/path/to/sample_1_read_1.fq'
# - '/path/to/sample_1_read_2.fq'
# sample_name_2:
# - '/path/to/sample_2_read_1.fq'
# - '/path/to/sample_2_read_2.fq'
blocklist: ''
mapability_bigwig: '/path/to/IRIS_data/resources/mappability/wgEncodeCrgMapabilityAlign24mer.bigWig'
mhc_list: '/path/to/example/hla_types_test.list'
mhc_by_sample: '/path/to/example/hla_patient_test.tsv'
gene_exp_matrix: ''
splice_matrix_txt: '/path/to/example/splicing_matrix/splicing_matrix.SE.cov10.NEPC_example.txt'
splice_matrix_idx: '/path/to/example/splicing_matrix/splicing_matrix.SE.cov10.NEPC_example.txt.idx'
sjc_count_txt: '/path/to/example/sjc_matrix/SJ_count.NEPC_example.txt'
sjc_count_idx: '/path/to/example/sjc_matrix/SJ_count.NEPC_example.txt.idx'
# Reference files
gtf_name: 'gencode.v26lift37.annotation.gtf'
fasta_name: 'ucsc.hg19.fasta'
reference_files:
gencode.v26lift37.annotation.gtf.gz:
url: 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/GRCh37_mapping/gencode.v26lift37.annotation.gtf.gz'
ucsc.hg19.fasta.gz:
url: 'http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz'
# Additional configuration
# rmats_path: '/path/to/conda_env_2/bin/rmats.py' # should be written by ./install
# conda_wrapper: '/path/to/conda_wrapper' # should be written by ./install
# conda_env_2: '/path/to/conda_env_2' # should be written by ./install
# conda_env_3: '/path/to/conda_env_3' # should be written by ./install
# iris_data: '/path/to/IRIS_data # should be written by ./install
# iedb_path: '/path/to/IEDB/mhc_i/src' # should be written by ./install