wf_params.yml

reference:
  class: File
  path: Homo_sapiens_assembly38.fasta
  format: http://edamontology.org/format_1929
sortsam_max_records_in_ram: 5000000
sortsam_java_options: -XX:-UseContainerSupport -Xmx8g -Xms8g
gatk4_MarkDuplicates_java_option: -XX:-UseContainerSupport -Xmx32g -Xms32g
gatk4_BaseRecalibrator_java_options: -XX:-UseContainerSupport -Xmx8g -Xms8g
gatk4_ApplyBQSR_java_options: -XX:-UseContainerSupport -Xmx8g -Xms8g
gatk4_HaplotypeCaller_java_options: -XX:-UseContainerSupport -Xmx8g -Xms8g
fastq2bam_ram_min: 48000
fastq2bam_cores_min: 16
bams2cram_ram_min: 48000
bams2cram_cores_min: 6
haplotypecaller_ram_min: 48000
haplotypecaller_cores_min: 6
bwa_bases_per_batch: 10000000
use_bqsr: true
dbsnp:
  class: File
  path: Homo_sapiens_assembly38.dbsnp138.vcf
  format: http://edamontology.org/format_3016
mills:
  class: File
  path: Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  format: http://edamontology.org/format_3016
known_indels:
  class: File
  path: Homo_sapiens_assembly38.known_indels.vcf.gz
  format: http://edamontology.org/format_3016
haplotypecaller_autosome_PAR_interval_bed:
  class: File
  path: autosome-PAR.bed
  format: http://edamontology.org/format_3584
haplotypecaller_autosome_PAR_interval_list:
  class: File
  path: autosome-PAR.interval_list
haplotypecaller_chrX_nonPAR_interval_bed:
  class: File
  path: chrX-nonPAR.bed
  format: http://edamontology.org/format_3584
haplotypecaller_chrX_nonPAR_interval_list:
  class: File
  path: chrX-nonPAR.interval_list
haplotypecaller_chrY_nonPAR_interval_bed:
  class: File
  path: chrY-nonPAR.bed
  format: http://edamontology.org/format_3584
haplotypecaller_chrY_nonPAR_interval_list:
  class: File
  path: chrY-nonPAR.interval_list
sample_id: NA19023
runlist_pe:
  - run_id: ERR1347662
    platform_name: ILLUMINA
    fastq1:
      class: File
      path: ERR1347662.small_1.fastq.gz
      format: http://edamontology.org/format_1930
    fastq2:
      class: File
      path: ERR1347662.small_2.fastq.gz
      format: http://edamontology.org/format_1930
runlist_se: []