<commit_before>---
## Environment
analysis_constant_path: analysis
max_cores_per_node: 36
node_ram_memory: 180
project_id: test
load_env:
  MIP_rd_rna:
    method: conda
    mip:
slurm_quality_of_service: low
## Input
pedigree_file: cluster_constant_path!/case_id!/case_id!_pedigree.yaml
reference_dir: cluster_constant_path!/references
## Output
config_file_analysis: cluster_constant_path!/case_id!/analysis/case_id!_config.yaml
outdata_dir: cluster_constant_path!/case_id!/analysis_constant_path!
outscript_dir: cluster_constant_path!/case_id!/analysis_constant_path!/scripts
sample_info_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml
## References
human_genome_reference: grch37_homo_sapiens_-d5-.fasta
qccollect_eval_metric_file: qc_eval_metric_-v1.1-.yaml
qccollect_regexp_file: qc_regexp_-v1.25-.yaml
star_fusion_genome_lib_dir: cluster_constant_path!/references/grch37_v19_CTAT_lib_Feb092018
transcript_annotation: grch37_gencode_annotation_reformated_-v31-.gtf
### Analysis
## Programs
## Parameters
arriba_blacklist_path: /arriba_v1.1.0/database/blacklist_hg19_hs37d5_GRCh37_2018-11-04.tsv.gz
arriba_cytoband_path: /arriba_v1.1.0/database/cytobands_hg19_hs37d5_GRCh37_2018-02-23.tsv
arriba_proteindomain_path: /arriba_v1.1.0/database/protein_domains_hg19_hs37d5_GRCh37_2018-03-06.gff3
picardtools_path: /usr/picard
qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml
vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-99/cache/<commit_msg>feat(arriba): config update<commit_after>---
## Environment
analysis_constant_path: analysis
max_cores_per_node: 36
node_ram_memory: 180
project_id: test
load_env:
  MIP_rd_rna:
    method: conda
    mip:
slurm_quality_of_service: low
## Input
pedigree_file: cluster_constant_path!/case_id!/case_id!_pedigree.yaml
reference_dir: cluster_constant_path!/references
## Output
config_file_analysis: cluster_constant_path!/case_id!/analysis/case_id!_config.yaml
outdata_dir: cluster_constant_path!/case_id!/analysis_constant_path!
outscript_dir: cluster_constant_path!/case_id!/analysis_constant_path!/scripts
sample_info_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml
## References
human_genome_reference: grch37_homo_sapiens_-d5-.fasta
qccollect_eval_metric_file: qc_eval_metric_-v1.1-.yaml
qccollect_regexp_file: qc_regexp_-v1.25-.yaml
star_fusion_genome_lib_dir: cluster_constant_path!/references/grch37_v19_CTAT_lib_Feb092018
transcript_annotation: grch37_gencode_annotation_reformated_-v31-.gtf
### Analysis
## Programs
## Parameters
arriba_blacklist_path: /arriba_v1.2.0/database/blacklist_hg19_hs37d5_GRCh37_2018-11-04.tsv.gz
arriba_cytoband_path: /arriba_v1.2.0/database/cytobands_hg19_hs37d5_GRCh37_2018-02-23.tsv
arriba_proteindomain_path: /arriba_v1.2.0/database/protein_domains_hg19_hs37d5_GRCh37_2019-07-05.gff3
picardtools_path: /usr/picard
qccollect_sampleinfo_file: cluster_constant_path!/case_id!/analysis_constant_path!/case_id!_qc_sample_info.yaml
vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/MIP_rd_rna/ensembl-tools-99/cache/
{'fraction_non_alphanumeric': 0.09025608994378513, 'fraction_numerical': 0.05246720799500312, 'mean_word_length': 9.641196013289036, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4491059', 'n_tokens_mistral': 1378, 'n_tokens_neox': 1233, 'n_words': 115}