Fq

fqlint

description: Performs quality control on the input FASTQs to ensure proper formatting
outputs: {'check': 'A string indicating whether the input FASTQs passed validation'}

_runtime (Any, required)
read_one_fastq (File, required); description: Input FASTQ with read one. Can be gzipped or uncompressed.; stream: true

read_two_fastq (File?); description: Input FASTQ with read two. Can be gzipped or uncompressed.; stream: true

disable_validator_codes (Array[String], default=[]); description: Array of codes to disable specific validators; choices: {'S001': "Plus line starts with a '+'", 'S002': "All characters in sequence line are one of 'ACGTN', case-insensitive", 'S003': "Name line starts with an '@'", 'S004': 'All four record lines (name, sequence, plus line, and quality) are present', 'S005': 'Sequence and quality lengths are the same', 'S006': "All characters in quality line are between '!' and '~' (ordinal values)", 'S007': 'All record names are unique', 'P001': 'Each paired read name is the same, excluding interleave'}
modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
modify_memory_gb (Int, default=0): Add to or subtract from dynamic memory allocation. Default memory is determined by the size of the inputs. Specified in GB.
paired_read_validation_level (String, default="high"); description: Only use paired read validators up to a given level; choices: ['low', 'medium', 'high']
panic (Boolean, default=true); description: Panic on first error (true) or log all errors (false)?; common: true
single_read_validation_level (String, default="high"); description: Only use single read validators up to a given level; choices: ['low', 'medium', 'high']

description: Subsamples the input FASTQ(s)
outputs: {'subsampled_read1': 'Gzipped FASTQ file containing subsampled read1', 'subsampled_read2': 'Gzipped FASTQ file containing subsampled read2'}

_runtime (Any, required)
read_one_fastq (File, required): Input FASTQ with read one. Can be gzipped or uncompressed.

read_two_fastq (File?): Input FASTQ with read two. Can be gzipped or uncompressed.

modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
prefix (String, default=sub(basename(read_one_fastq),"([_\.][rR][12])?(\.subsampled)?\.(fastq|fq)(\.gz)?$","")): Prefix for the output FASTQ file(s). The extension _R1.subsampled.fastq.gz and _R2.subsampled.fastq.gz will be added.
probability (Float, default=1.0); description: The probability a record is kept, as a decimal (0.0, 1.0). Cannot be used with record-count. Any probability<=0.0 or probability>=1.0 to disable.; common: true
record_count (Int, default=-1); description: The exact number of records to keep. Cannot be used with probability. Any record_count<=0 to disable.; common: true