Workflow
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
workflows/general/bam-to-fastqs.wdlRUN WITH
sprocket run --target bam_to_fastqs workflows/general/bam-to-fastqs.wdlworkflows\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]if paired_end
then select_all(bam_to_f...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)
