BAM to FASTQs
Converts an input BAM file to one or more FASTQ files, performing QC checks along the way
WDL Version
1.1
Category
Utility
Nested Inputs Allowed
RUN WITH
sprocket run workflows/general/bam-to-fastqs.wdl [INPUTS]...
Inputs
Required Inputs
Name
Type
Description
bamFileBAM file to split into FASTQs
BAM file to split into FASTQs
Other Inputs
Name
Type
Default
Description
paired_endBooleantrueIs the data Paired-End (true) or Single-End (false)?
Is the data Paired-End (true) or Single-End (false)?
use_all_coresBooleanfalseUse all cores for multi-core steps?
Use all cores for multi-core steps?
Outputs
Name
Type
Expression
Description
read1sArray[File]select_all(bam_to_fastq.read_one_fastq_gz)Array of FASTQ files corresponding to either
first reads (if paired_end = true) or all reads (if paired_end = false)Array of FASTQ files corresponding to either
first reads (if paired_end = true) or all reads (if paired_end = false)read2sArray[File?]bam_to_fastq.read_two_fastq_gzArray of FASTQ files corresponding to
last reads (if paired_end = true)Array of FASTQ files corresponding to
last reads (if paired_end = true)