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config.yaml
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config.yaml
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# Inputs
ref_fna_file: ../sequences/alignment_reference/GCF_000182965.3/GCF_000182965.3_ASM18296v3_genomic.fa
ref_fna_dict: ../sequences/alignment_reference/GCF_000182965.3/GCF_000182965.3_ASM18296v3_genomic.dict
ref_fna_fai: ../sequences/alignment_reference/GCF_000182965.3/GCF_000182965.3_ASM18296v3_genomic.fa.fai
ref_fna_indexing_log: ../sequences/alignment_reference/GCF_000182965.3/GCF_000182965.3_ASM18296v3_genomic.fa.gz.indexing.log
reads_dir: ../sequences/reads/
fastq_screen_references: ../sequences/screens
adapters: ../sequences/adapter/TruSeq3-PE-2.fa
read_group_script: ./read_group.sh
# Outputs
preqc_dir: ../outputs/quality_control/preqc/
adaptrim_dir: ../outputs/quality_control/adaptrim_bbduk/
adaptrim_qc_dir: ../outputs/quality_control/adaptrim_bbduk_qc/
adaptrim_qualtrim_dir: ../outputs/quality_control/adaptrim_qualtrim/
adaptrim_qualtrim_qc_dir: ../outputs/quality_control/adaptrim_qualtrim_qc/
fastq_screen_conf: ./fastq_screen.conf
fastq_screen_logfile_extension: '_fastq_screen.log'
screening_dir: ../outputs/quality_control/adaptrim_qualtrim/screening/
snakemake_logs: ./job_logs/
samtools_reports_dir: ../outputs/quality_control/samtools_reports/
aligned_bam_dir: ../outputs/aligned_bams/
#merged_bam_dir: ../outputs/merged_bams
picard_dir: ../outputs/quality_control/picard/
combined_dir: ../outputs/combined/
combined_gvcf: ../outputs/combined/cohort.g.vcf.gz
combined_vcf: ../coutputs/combined/cohort.vcf.gz
gvcfs_dir: ../outputs/gvcfs/
# File formatting
read1_tag: 'R1'
read2_tag: 'R2'
adaptrim1_tag: '.adaptrim.1P'
adaptrim2_tag: '.adaptrim.2P'
qualtrim_p_tag: '_P'
qualtrim_u_tag: '_U'
#fastqc does not support output file name
#adaptrim_qualtrim_1p_tag: '.adaptrim.qualtrim_1P'
#adaptrim_qualtrim_2p_tag: '.adaptrim.qualtrim_2P'
# Extensions
reads_file_extension: '.fastq.gz'
preqc_file_extension: '_fastqc.zip'
adaptrim_file_extension: '.fq.gz'
adaptrim_qc_file_extension: '_fastqc.zip'
adaptrim_qualtrim_file_extension: '.adaptrim.qualtrim.fq.gz'
adaptrim_qualtrim_qc_file_extension: '.adaptrim.qualtrim_fastqc.zip'
adaptrim_qualtrim_qc_html_file_extension: '.adaptrim.qualtrim_fastqc.html'
aligned_bam_file_extension: '_sorted.bam'
aligned_bam_flagstat_file_extension: '_sorted.flagstat.txt'
indexed_aligned_bam_file_extension: '_sorted.bam.bai'
picard_file_extension: '_sorted_rmdups.bam'
picard_rpt_file_extension: '_sorted_DuplicationMetrics.txt'
gvcfs_file_extension: '.g.vcf.gz'
vcfs_file_extension: '.vcf.gz'