class Input:
"""Input fields for GatkHaplotypeCallerGvcf."""
bam = DataField("alignment:bam", label="Analysis ready BAM file")
ref_seq = DataField("seq:nucleotide", label="Reference sequence")
advanced = BooleanField(
label="Show advanced options",
description="Inspect and modify parameters.",
default=False,
)
class Options:
"""Options."""
intervals = DataField(
"bed",
label=
"Use intervals BED file to limit the analysis to the specified parts of the genome.",
required=False,
)
contamination = FloatField(
label="Contamination fraction",
default=0,
description=
"Fraction of contamination in sequencing data (for all samples) to aggressively remove.",
)
options = GroupField(Options, label="Options", hidden="!advanced")
class Input:
"""Input fields for SlamdunkAllPaired."""
reads = DataField('reads:fastq:paired', label='Reads')
transcriptome = DataField(
'seq:nucleotide',
label='FASTA file containig sequences for alingnig.')
regions = DataField(
'bed', label='BED file with coordinates of regions of interest.')
filter_multimappers = BooleanField(
label='Filter multimappers',
description=
'If true filter and reasign multimappers based on provided BED file with regions of interest.',
default=True)
max_alignments = IntegerField(
label='Maximum number of multimapper alignments',
description=
'The maximum number of alignments that will be reported for a multi-mapping read (i.e. reads'
'with multiple alignments of equal best scores).',
default=1)
read_length = IntegerField(
label='Maximum read length',
description='Maximul length of reads in the input FASTQ file.',
default=150)
class Input:
"""Input fields."""
data = DataField("test", label="My input data")
data2 = DataField("test",
label="My second non-required input data",
required=False)
class Input:
"""Input fields to process WgsPreprocess."""
reads = DataField("reads:fastq:paired", label="Input sample")
ref_seq = DataField("seq:nucleotide", label="Reference sequence")
bwa_index = DataField("index:bwa", label="BWA genome index")
known_sites = ListField(DataField("variants:vcf"),
label="Known sites of variation (VCF)")
advanced = BooleanField(
label="Show advanced options",
description="Inspect and modify parameters.",
default=False,
)
class AdvancedOptions:
"""Advanced options."""
pixel_distance = IntegerField(
label="--OPTICAL_DUPLICATE_PIXEL_DISTANCE",
default=2500,
description="Set the optical pixel distance, e.g. "
"distance between clusters. Modify this parameter to "
"ensure compatibility with older Illumina platforms.",
)
advanced_options = GroupField(AdvancedOptions,
label="Advanced options",
hidden="!advanced")
class Input:
"""Input fields for SlamdunkAllPaired."""
reads = DataField("reads:fastq:paired", label="Reads")
ref_seq = DataField("seq:nucleotide", label="FASTA file")
regions = DataField(
"bed", label="BED file with coordinates of regions of interest"
)
filter_multimappers = BooleanField(
label="Filter multimappers",
description="If true filter and reasign multimappers based on provided BED file with regions of interest",
default=True,
)
max_alignments = IntegerField(
label="Maximum number of multimapper alignments",
description="The maximum number of alignments that will be reported for a multi-mapping read (i.e. reads"
"with multiple alignments of equal best scores)",
default=1,
)
read_length = IntegerField(
label="Maximum read length",
description="Maximum length of reads in the input FASTQ file",
default=150,
)
class Input:
"""Input fields."""
my_field = StringField(label="My field")
my_list = ListField(StringField(), label="My list")
input_data = DataField("test:save", label="My input data")
input_entity_data = DataField("entity", label="My entity data")
bar = DataField(data_type="test:save", label="My bar")
url = UrlField(UrlField.DOWNLOAD, label="My URL")
integer = IntegerField(label="My integer")
my_float = FloatField(label="My float")
my_json = JsonField(label="Blah blah")
my_optional = StringField(label="Optional",
required=False,
default="default value")
my_optional_no_default = StringField(label="Optional no default",
required=False)
class MyGroup:
foo = IntegerField(label="Foo")
bar = StringField(label="Bar")
group_optional_no_default = StringField(
label="Group optional no default", required=False)
my_group = GroupField(MyGroup, label="My group")
class Input:
"""Input fields for BsConversionRate."""
mr = DataField(
"alignment:bam:walt",
label="Aligned reads from bisulfite sequencing",
description="Bisulfite specifc alignment such as WALT is required as .mr file type is used. Duplicates"
"should be removed to reduce any bias introduced by incomplete conversion on PCR duplicate"
"reads.",
)
skip = BooleanField(
label="Skip Bisulfite conversion rate step",
description="Bisulfite conversion rate step can be skipped.",
default=False,
)
sequence = DataField(
"seq:nucleotide",
label="Unmethylated control sequence",
description="Separate unmethylated control sequence FASTA file is required to estimate bisulfite"
"conversion rate.",
required=False,
)
count_all = BooleanField(
label="Count all cytosines including CpGs", default=True
)
read_length = IntegerField(label="Average read length", default=150)
max_mismatch = FloatField(
label="Maximum fraction of mismatches", required=False
)
a_rich = BooleanField(label="Reads are A-rich", default=False)
class Input:
"""Input fields for AlleyoopRates."""
ref_seq = DataField(
"seq:nucleotide",
label="FASTA file containig sequences for aligning")
slamdunk = DataField("alignment:bam:slamdunk",
label="Slamdunk results")
class Input:
"""Input fields to process ROSE2."""
input_macs = DataField(
"chipseq:callpeak",
label="BED/narrowPeak file (MACS results)",
required=False,
hidden="input_upload",
)
input_upload = DataField(
"bed",
label="BED file (Upload)",
required=False,
hidden="input_macs || use_filtered_bam",
)
use_filtered_bam = BooleanField(
label="Use Filtered BAM File",
default=False,
hidden="input_upload",
description=("Use filtered BAM file from a MACS2 object to rank "
"enhancers by. Only applicable if input is MACS2."),
)
rankby = DataField(
"alignment:bam",
label="BAM file",
required=False,
hidden="use_filtered_bam",
description="BAM file to rank enhancers by.",
)
control = DataField(
"alignment:bam",
label="Control BAM File",
required=False,
hidden="use_filtered_bam",
description="BAM file to rank enhancers by.",
)
tss = IntegerField(
label="TSS exclusion",
default=0,
description=
"Enter a distance from TSS to exclude. 0 = no TSS exclusion.",
)
stitch = IntegerField(
label="Stitch",
required=False,
description=(
"Enter a max linking distance for stitching. If not "
"given, optimal stitching parameter will be determined"
" automatically."),
)
mask = DataField(
"bed",
label="Masking BED file",
required=False,
description=(
"Mask a set of regions from analysis. Provide a BED of"
" masking regions."),
)
class Input:
"""Input fields to process ChipQC."""
alignment = DataField(
data_type="alignment:bam",
label="Aligned reads",
)
peaks = DataField(
data_type="chipseq:callpeak",
label="Called peaks",
)
blacklist = DataField(
data_type="bed",
label="Blacklist regions",
description="BED file containing genomic regions that should be "
"excluded from the analysis.",
required=False,
)
calculate_enrichment = BooleanField(
label="Calculate enrichment",
description="Calculate enrichment of signal in known genomic "
"annotation. By default annotation is provided from "
"the TranscriptDB package specified by genome bulid "
"which should match one of the supported annotations "
"(hg19, hg38, hg18, mm10, mm9, rn4, ce6, dm3). If "
"annotation is not supported the analysis is skipped.",
default=False,
)
class Advanced:
"""Add advanced list of options."""
quality_threshold = IntegerField(
label="Mapping quality threshold",
description="Only reads with mapping quality scores above "
"this threshold will be used for some statistics.",
default=15,
)
profile_window = IntegerField(
label="Window size",
description="An integer indicating the width of the window "
"used for peak profiles. Peaks will be centered "
"on their summits and include half of the window "
"size upstream and half downstream of this point.",
default=400,
)
shift_size = StringField(
label="Shift size",
description="Vector of values to try when computing optimal "
"shift sizes. It should be specifeird as "
"consecutive numbers vector with start:end",
default="1:300",
)
advanced = GroupField(
Advanced,
label="Advanced parameters",
)
class Input:
"""Input fields to process Bamclipper."""
alignment = DataField('alignment:bam', label='Alignment BAM file')
bedpe = DataField('bedpe', label='BEDPE file', required=False)
skip = BooleanField(
label='Skip Bamclipper step',
description='Use this option to skip Bamclipper step.',
default=False)
class Input:
"""Input fields to process ImportScRNA10x."""
reads = DataField(
data_type="screads:10x:",
label="10x reads data object",
)
genome_index = DataField(
data_type="genomeindex:10x:",
label="10x genome index data object",
)
chemistry = StringField(
label="Chemistry",
required=False,
default="auto",
description=
("Assay configuration. By default the assay configuration is detected "
"automatically, which is the recommended mode. You should only specify "
"chemistry if there is an error in automatic detection."),
choices=[
("auto", "auto"),
("Single Cell 3'", "threeprime"),
("Single Cell 5'", "fiveprime"),
("Single Cell 3' v1", "SC3Pv1"),
("Single Cell 3' v2", "SC3Pv2"),
("Single Cell 3' v3", "SC3Pv3"),
("Single Cell 5' paired-end", "C5P-PE"),
("Single Cell 5' R2-only", "SC5P-R2"),
],
)
trim_r1 = IntegerField(
label="Trim R1",
required=False,
description=
("Hard-trim the input R1 sequence to this length. Note that the length "
"includes the Barcode and UMI sequences so do not set this below 26 for "
"Single Cell 3' v2 or Single Cell 5'. This and \"Trim R2\" are useful for "
"determining the optimal read length for sequencing."),
)
trim_r2 = IntegerField(
label="Trim R2",
required=False,
description="Hard-trim the input R2 sequence to this length.",
)
expected_cells = IntegerField(
label="Expected number of recovered cells",
default=3000,
)
force_cells = IntegerField(
label="Force cell number",
required=False,
description=
("Force pipeline to use this number of cells, bypassing the cell "
"detection algorithm. Use this if the number of cells estimated by Cell "
"Ranger is not consistent with the barcode rank plot."),
)
class Input:
"""Input fields for GatkGenotypeGVCFs."""
gvcfs = ListField(
DataField("variants:gvcf"),
label="Input data (GVCF)",
)
ref_seq = DataField("seq:nucleotide", label="Reference sequence")
intervals = DataField(
"bed",
label="Intervals file (.bed)",
)
dbsnp = DataField("variants:vcf", label="dbSNP file")
advanced = BooleanField(
label="Show advanced options",
description="Inspect and modify parameters.",
default=False,
)
class AdvancedOptions:
"""Advanced options."""
batch_size = IntegerField(
label="Batch size",
default=0,
description="Batch size controls the number of samples "
"for which readers are open at once and therefore provides "
"a way to minimize memory consumption. However, it can "
"take longer to complete. Use the consolidate flag if more "
"than a hundred batches were used. This will improve feature "
"read time. batchSize=0 means no batching "
"(i.e. readers for all samples will be opened at once).",
)
consolidate = BooleanField(
label="Consolidate",
default=False,
description="Boolean flag to enable consolidation. If "
"importing data in batches, a new fragment is created for "
"each batch. In case thousands of fragments are created, "
"GenomicsDB feature readers will try to open ~20x as many "
"files. Also, internally GenomicsDB would consume more "
"memory to maintain bookkeeping data from all fragments. "
"Use this flag to merge all fragments into one. Merging "
"can potentially improve read performance, however overall "
"benefit might not be noticeable as the top Java layers "
"have significantly higher overheads. This flag has no "
"effect if only one batch is used.",
)
advanced_options = GroupField(AdvancedOptions,
label="Advanced options",
hidden="!advanced")
class Input:
"""Input fields to process Bamclipper."""
alignment = DataField("alignment:bam", label="Alignment BAM file")
bedpe = DataField("bedpe", label="BEDPE file", required=False)
skip = BooleanField(
label="Skip Bamclipper step",
description="Use this option to skip Bamclipper step.",
default=False,
)
class Input:
"""Input fields to process CellRangerMkref."""
genome = DataField(
data_type='genome:fasta:',
label='Reference genome',
)
annotation = DataField(
data_type='annotation:gtf:',
label='Annotation',
)
class Input:
"""Input fields to process CellRangerMkref."""
genome = DataField(
data_type="seq:nucleotide:",
label="Reference genome",
)
annotation = DataField(
data_type="annotation:gtf:",
label="Annotation",
)
class Input:
"""Input fields for InsertSizeMetrics."""
bam = DataField("alignment:bam", label="Alignment BAM file")
genome = DataField("seq:nucleotide", label="Genome")
minimum_fraction = FloatField(
label="Minimum fraction of reads in a category to be considered ",
description="When generating the histogram, discard any data "
"categories (out of FR, TANDEM, RF) that have fewer than this "
"fraction of overall reads (Range: 0 and 0.5).",
default=0.05,
)
include_duplicates = BooleanField(
label=
"Include reads marked as duplicates in the insert size histogram",
default=False,
)
deviations = FloatField(
label="Deviations limit",
description=
"Generate mean, standard deviation and plots by trimming "
"the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. "
"This is done because insert size data typically includes enough "
"anomalous values from chimeras and other artifacts to make the "
"mean and standard deviation grossly misleading regarding the real "
"distribution.",
default=10.0,
)
validation_stringency = StringField(
label="Validation stringency",
description="Validation stringency for all SAM files read by this "
"program. Setting stringency to SILENT can improve "
"performance when processing a BAM file in which "
"variable-length data (read, qualities, tags) do not "
"otherwise need to be decoded. Default is STRICT.",
choices=[
("STRICT", "STRICT"),
("LENIENT", "LENIENT"),
("SILENT", "SILENT"),
],
default="STRICT",
)
assume_sorted = BooleanField(
label="Sorted BAM file",
description=
"If True, the sort order in the header file will be ignored.",
default=False,
)
class Input:
"""Input fields for AlleyoopSnpEval."""
ref_seq = DataField(
"seq:nucleotide",
label="FASTA file containig sequences for aligning")
regions = DataField(
"bed", label="BED file with coordinates of regions of interest")
slamdunk = DataField("alignment:bam:slamdunk",
label="Slamdunk results")
read_length = IntegerField(
label="Maximum read length",
description="Maximum length of reads in the input FASTQ file",
default=150,
)
class Input:
"""Input fields for AlignmentSummary."""
bam = DataField("alignment:bam", label="Alignment BAM file")
genome = DataField("seq:nucleotide", label="Genome")
adapters = DataField("seq:nucleotide",
label="Adapter sequences",
required=False)
validation_stringency = StringField(
label="Validation stringency",
description="Validation stringency for all SAM files read by this "
"program. Setting stringency to SILENT can improve "
"performance when processing a BAM file in which "
"variable-length data (read, qualities, tags) do not "
"otherwise need to be decoded. Default is STRICT.",
choices=[
("STRICT", "STRICT"),
("LENIENT", "LENIENT"),
("SILENT", "SILENT"),
],
default="STRICT",
)
insert_size = IntegerField(label="Maximum insert size", default=100000)
pair_orientation = StringField(
label="Pair orientation",
default="null",
choices=[
("null", "Unspecified"),
("FR", "FR"),
("RF", "RF"),
("TANDEM", "TANDEM"),
],
)
bisulfite = BooleanField(
label="BAM file consists of bisulfite sequenced reads",
default=False)
assume_sorted = BooleanField(
label="Sorted BAM file",
description=
"If true the sort order in the header file will be ignored.",
default=False,
)
class Input:
"""Input fields to perform Base quality score recalibration."""
bam = DataField("alignment:bam", label="BAM file containing reads")
reference = DataField("seq:nucleotide", label="Reference genome file")
known_sites = ListField(
DataField(
data_type="variants:vcf",
description=
"One or more databases of known polymorphic sites used to exclude regions around known "
"polymorphisms from analysis.",
),
label="List of known sites of variation",
)
intervals = DataField(
data_type="bed",
required=False,
label="One or more genomic intervals over which to operate.",
description=
"This field is optional, but it can speed up the process by restricting calculations to "
"specific genome regions.",
)
read_group = StringField(
label="Replace read groups in BAM",
description=
"Replace read groups in a BAM file.This argument enables the user to replace all read groups "
"in the INPUT file with a single new read group and assign all reads to this read group in "
"the OUTPUT BAM file. Addition or replacement is performed using Picard's "
"AddOrReplaceReadGroups tool. Input should take the form of -name=value delimited by a "
'";", e.g. "-ID=1;-LB=GENIALIS;-PL=ILLUMINA;-PU=BARCODE;-SM=SAMPLENAME1". See tool\'s '
"documentation for more information on tag names. Note that PL, LB, PU and SM are require "
"fields. See caveats of rewriting read groups in the documentation.",
default="",
)
validation_stringency = StringField(
label="Validation stringency",
description=
"Validation stringency for all SAM files read by this program. Setting stringency to SILENT "
"can improve performance when processing a BAM file in which variable-length data (read, "
"qualities, tags) do not otherwise need to be decoded. Default is STRICT. This setting is "
"used in BaseRecalibrator and ApplyBQSR processes.",
choices=[
("STRICT", "STRICT"),
("LENIENT", "LENIENT"),
("SILENT", "SILENT"),
],
default="STRICT",
)
class Input:
"""Input fields to process MergeFastqPaired."""
reads = ListField(
DataField(data_type="reads:fastq:paired:"),
label="Reads data objects",
)
class Input:
"""Input fields to process MergeFastqSingle."""
reads = ListField(
DataField(data_type="reads:fastq:single:"),
label="Reads data objects",
)
class Options:
"""Options."""
stranded = StringField(
label="Assay type",
default='non_specific',
choices=[
('non_specific', 'Strand non-specific'),
('forward', 'Strand-specific forward'),
('reverse', 'Strand-specific reverse'),
('auto', 'Detect automatically'),
],
)
cdna_index = DataField('index:salmon',
label="cDNA index file",
required=False,
hidden="options.stranded != 'auto'")
n_reads = IntegerField(
label="Number of reads in subsampled alignment file",
default=5000000,
hidden="options.stranded != 'auto'")
maxPhredScore = IntegerField(
label="Max Phred Score",
required=False,
)
adjustPhredScore = IntegerField(
label="Adjust Phred Score",
required=False,
)
class Input:
"""Input fields to process MapMicroarrayProbes."""
expressions = ListField(
DataField("microarray:normalized"),
label="Normalized expressions",
)
mapping_file = FileField(
label="File with probe ID mappings",
description=
"The file should be tab-separated and contain two columns with their column names. The first "
"column should contain Gene IDs and the second one should contain probe names. Supported file extensions "
"are .tab.*, .tsv.*, .txt.*",
required=False,
)
source = StringField(
label="Gene ID source",
description=
"Gene ID source used for probe mapping is required when using a custom file.",
allow_custom_choice=True,
required=False,
choices=[
("AFFY", "AFFY"),
("DICTYBASE", "DICTYBASE"),
("ENSEMBL", "ENSEMBL"),
("NCBI", "NCBI"),
("UCSC", "UCSC"),
],
)
build = StringField(
label="Genome build",
description=
"Genome build of mapping file is required when using a custom file.",
required=False,
)
class Input:
"""Input fields to process ClusterTimeCourse."""
expressions = ListField(
DataField("expression"),
relation_type="series",
label="Time series relation",
description=
"Select time course to which the expressions belong to.",
)
genes = ListField(
StringField(),
label="Gene subset",
required=False,
description="Select at least two genes or leave this field empty.",
)
gene_species = StringField(
label="Species",
description="Species to which the selected genes belong to. "
"This field is required if gene subset is set.",
required=False,
hidden="!genes",
allow_custom_choice=True,
choices=[
("Dictyostelium discoideum", "Dictyostelium discoideum"),
("H**o sapiens", "H**o sapiens"),
("Macaca mulatta", "Macaca mulatta"),
("Mus musculus", "Mus musculus"),
("Rattus norvegicus", "Rattus norvegicus"),
],
)
gene_source = StringField(
label="Gene ID database of selected genes",
description="This field is required if gene subset is set.",
required=False,
hidden="!genes",
)
distance = StringField(
label="Distance metric",
choices=[
("spearman", "Spearman"),
("pearson", "Pearson"),
],
default="spearman",
)
linkage = StringField(
label="Linkage method",
choices=[
("single", "single"),
("average", "average"),
("complete", "complete"),
],
default="average",
)
ordering = BooleanField(
label="Use optimal ordering",
description="Results in a more intuitive tree structure, "
"but may slow down the clustering on large datasets",
default=False,
)
class Input:
"""Input fields to process MicroarrayExpression."""
exp_unmapped = DataField(
"microarray:normalized",
label="Unmapped normalized expressions",
description=
"Unmapped normalized expression with the original probe IDs.",
)
exp = FileField(
label="Normalized and mapped expressions file",
description=
"Files should have two columns one with GeneIDs and the other one with expression values."
"Expected column names are 'Gene' and 'Expression'.Supported file extensions are .tab.*, .tsv.*, .txt.*",
)
source = StringField(
label="Gene ID source",
allow_custom_choice=True,
choices=[
("AFFY", "AFFY"),
("DICTYBASE", "DICTYBASE"),
("ENSEMBL", "ENSEMBL"),
("NCBI", "NCBI"),
("UCSC", "UCSC"),
],
)
build = StringField(label="Genome build", )
probe_mapping = StringField(label="Probe to transcript mapping used", )
class Input:
"""Input fields for CollectRrbsMetrics."""
bam = DataField("alignment:bam", label="Alignment BAM file")
genome = DataField("seq:nucleotide", label="Genome")
min_quality = IntegerField(
label=
"Threshold for base quality of a C base before it is considered",
default=20,
)
next_base_quality = IntegerField(
label=
"Threshold for quality of a base next to a C before the C base is considered",
default=10,
)
min_lenght = IntegerField(label="Minimum read length", default=5)
mismatch_rate = FloatField(
label=
"Maximum fraction of mismatches in a read to be considered (Range: 0 and 1)",
default=0.1,
)
validation_stringency = StringField(
label="Validation stringency",
description="Validation stringency for all SAM files read by this "
"program. Setting stringency to SILENT can improve "
"performance when processing a BAM file in which "
"variable-length data (read, qualities, tags) do not "
"otherwise need to be decoded. Default is STRICT.",
choices=[
("STRICT", "STRICT"),
("LENIENT", "LENIENT"),
("SILENT", "SILENT"),
],
default="STRICT",
)
assume_sorted = BooleanField(
label="Sorted BAM file",
description=
"If true the sort order in the header file will be ignored.",
default=False,
)
class Input:
"""Input fields to process MethylationArraySesame."""
idat_file = DataField(
data_type="methylationarray:idat",
label="Illumina methylation array IDAT file",
description="Illumina methylation array BeadChip raw IDAT file.",
)
class Input:
"""Input fields."""
alignment = DataField("alignment:bam", label="Alignment")
annotation = DataField("annotation:gtf", label="GTF annotation")
class Options:
"""Options."""
stranded = StringField(
label="Assay type",
default="non_specific",
choices=[
("non_specific", "Strand non-specific"),
("forward", "Strand-specific forward"),
("reverse", "Strand-specific reverse"),
("auto", "Detect automatically"),
],
)
cdna_index = DataField(
"index:salmon",
label="cDNA index file",
required=False,
hidden="options.stranded != 'auto'",
)
n_reads = IntegerField(
label="Number of reads in subsampled alignment file",
default=5000000,
hidden="options.stranded != 'auto'",
)
maxPhredScore = IntegerField(
label="Max Phred Score",
required=False,
)
adjustPhredScore = IntegerField(
label="Adjust Phred Score",
required=False,
)
options = GroupField(Options, label="Options")
class Input:
"""Input fields to perform Base quality score recalibration."""
bam = DataField('alignment:bam', label='BAM file containing reads')
reference = DataField('genome:fasta', label='Reference genome file')
known_sites = ListField(
DataField(
data_type='variants:vcf',
description=
'One or more databases of known polymorphic sites used to exclude regions around known '
'polymorphisms from analysis.'),
label='List of known sites of variation',
)
intervals = DataField(
data_type='bed',
label='One or more genomic intervals over which to operate.',
description=
'This field is optional, but it can speed up the process by restricting calculations to '
'specific genome regions.')
read_group = StringField(
label='Replace read groups in BAM',
description=
'Replace read groups in a BAM file.This argument enables the user to replace all read groups '
'in the INPUT file with a single new read group and assign all reads to this read group in '
'the OUTPUT BAM file. Addition or replacement is performed using Picard\'s '
'AddOrReplaceReadGroups tool. Input should take the form of -name=value delimited by a '
'";", e.g. "-ID=1;-LB=GENIALIS;-PL=ILLUMINA;-PU=BARCODE;-SM=SAMPLENAME1". See tool\'s '
'documentation for more information on tag names. Note that PL, LB, PU and SM are require '
'fields. See caveats of rewriting read groups in the documentation.',
default='')
validation_stringency = StringField(
label='Validation stringency',
description=
'Validation stringency for all SAM files read by this program. Setting stringency to SILENT '
'can improve performance when processing a BAM file in which variable-length data (read, '
'qualities, tags) do not otherwise need to be decoded. Default is STRICT. This setting is '
'used in BaseRecalibrator and ApplyBQSR processes.',
choices=[
('STRICT', 'STRICT'),
('LENIENT', 'LENIENT'),
('SILENT', 'SILENT'),
],
default='STRICT',
)
