Bam to fastqs

bam_to_fastqs

description: Converts an input BAM file to one or more FASTQ files, performing QC checks along the way
outputs: {'read1s': 'Array of FASTQ files corresponding to either first reads (if paired_end = true) or all reads (if paired_end = false)', 'read2s': 'Array of FASTQ files corresponding to last reads (if paired_end = true)'}
allowNestedInputs: true

paired_end (Boolean, default=true): Is the data Paired-End (true) or Single-End (false)?
use_all_cores (Boolean, default=false): Use all cores for multi-core steps?
bam_to_fastq.append_read_number (Boolean, default=true)
bam_to_fastq.bitwise_filter (FlagFilter, default={"include_if_all": "0x0", "exclude_if_any": "0x900", "include_if_any": "0x0", "exclude_if_all": "0x0"})
bam_to_fastq.collated (Boolean, default=false)
bam_to_fastq.fail_on_unexpected_reads (Boolean, default=false)
bam_to_fastq.fast_mode (Boolean, default=!retain_collated_bam)
bam_to_fastq.modify_disk_size_gb (Int, default=0)
bam_to_fastq.modify_memory_gb (Int, default=0)
bam_to_fastq.ncpu (Int, default=2)
bam_to_fastq.output_singletons (Boolean, default=false)
bam_to_fastq.prefix (String, default=basename(bam,".bam"))
bam_to_fastq.retain_collated_bam (Boolean, default=false)
fqlint.disable_validator_codes (Array[String], default=[])
fqlint.modify_disk_size_gb (Int, default=0)
fqlint.modify_memory_gb (Int, default=0)
fqlint.paired_read_validation_level (String, default="high")
fqlint.panic (Boolean, default=true)
fqlint.single_read_validation_level (String, default="high")
quickcheck.modify_disk_size_gb (Int, default=0)
split.modify_disk_size_gb (Int, default=0)
split.ncpu (Int, default=2)
split.prefix (String, default=basename(bam,".bam"))
split.reject_empty_output (Boolean, default=true)
split.reject_unaccounted_reads (Boolean, default=true)