def inputs(self) -> List[ToolInput]:
return [
ToolInput("piscesVersion", String()),
ToolInput(
"inputBam",
BamBai(),
prefix="-b",
position=4,
shell_quote=False,
doc="Input BAM file",
),
ToolInput(
"outputDir",
String(),
prefix="--outfolder",
position=4,
shell_quote=False,
doc="Output Folder",
),
ToolInput(
"referenceFolder",
Directory(),
prefix="--genomefolders",
position=5,
shell_quote=False,
doc="Folder containing reference genome files",
),
*self.additional_hygea_args,
]
def inputs(self):
return [
*StarAlignerBase.additional_inputs,
ToolInput("help", Boolean(optional=True), prefix="--help", doc="help page"),
ToolInput(
"runThreadN",
Int(optional=True),
default=CpuSelector(),
prefix="--runThreadN",
doc="int: number of threads to run STAR. Default: 1.",
),
ToolInput(
"genomeDir",
Directory(optional=True),
prefix="--genomeDir",
doc="string: path to the directory where genome files are stored (for –runMode alignReads) or will be generated (for –runMode generateGenome). Default: ./GenomeDir",
),
ToolInput(
"readFilesIn",
Array(FastqGz, optional=True),
prefix="--readFilesIn",
separator=",",
doc="string(s): paths to files that contain input read1 (and, if needed, read2). Default: Read1,Read2.",
),
ToolInput(
"outFileNamePrefix",
Filename(),
prefix="--outFileNamePrefix",
doc="string: output files name prefix (including full or relative path). Can only be defined on the command line.",
),
ToolInput(
"outSAMtype",
Array(String(), optional=True),
prefix="--outSAMtype",
separator=" ",
prefix_applies_to_all_elements=False,
doc='strings: type of SAM/BAM output. 1st word: "BAM": outputBAMwithoutsorting, "SAM": outputSAMwithoutsorting, "None": no SAM/BAM output. 2nd,3rd: "Unsorted": standard unsorted. "SortedByCoordinate": sorted by coordinate. This option will allocate extra memory for sorting which can be specified by –limitBAMsortRAM.',
),
ToolInput(
"outSAMunmapped",
String(optional=True),
prefix="--outSAMunmapped",
doc="string(s): output of unmapped reads in the SAM format",
),
ToolInput(
"outSAMattributes",
String(optional=True),
prefix="--outSAMattributes",
doc="string: a string of desired SAM attributes, in the order desired for the output SAM",
),
ToolInput(
"readFilesCommand",
String(optional=True),
prefix="--readFilesCommand",
doc="string(s): command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout",
),
]
def inputs(self):
return [
ToolInput(
"runFolderDir",
input_type=Directory(),
prefix="-R",
doc="path to runfolder directory",
),
ToolInput(
"sampleSheet",
input_type=Csv(),
prefix="--sample-sheet",
doc="path to the sample sheet",
),
ToolInput(
"loadingThreads",
input_type=Int(),
prefix="-r",
default=4,
doc="number of threads used for loading BCL data",
),
ToolInput(
"processingThreads",
input_type=Int(),
prefix="-p",
default=4,
doc="number of threads used for processing demultiplexed data",
),
ToolInput(
"writingThreads",
input_type=Int(),
prefix="-w",
default=4,
doc="number of threads used for writing FASTQ data",
),
*Bcl2FastqBase.additional_inputs,
]
def inputs(self) -> List[ToolInput]:
return [
ToolInput(
"inputFile",
CompressedVcf(),
prefix="--input_file",
doc="Input file name. Can use compressed file (gzipped).",
),
ToolInput(
"outputFilename",
Filename(
prefix=InputSelector("inputFile", remove_file_extension=True),
extension=".vcf",
),
prefix="--output_file",
doc="(-o) Output file name. Results can write to STDOUT by specifying "
' as the output file name - this will force quiet mode. Default = "variant_effect_output.txt"',
),
ToolInput(
"vcf",
Boolean(),
default=True,
prefix="--vcf",
doc="Writes output in VCF format. Consequences are added in the INFO field of the VCF file, using the "
'key "CSQ". Data fields are encoded separated by "|"; the order of fields is written in the VCF header.'
' Output fields in the "CSQ" INFO field can be selected by using --fields. If the input format was VCF,'
" the file will remain unchanged save for the addition of the CSQ field (unless using any filtering). "
"Custom data added with --custom are added as separate fields, using the key specified for each data "
"file. Commas in fields are replaced with ampersands (&) to preserve VCF format.",
),
# ToolInput('plugin', [PLUGINS](optional=True), prefix='--plugin',
# doc='Use named plugin. Plugin modules should be installed in the Plugins subdirectory of the VEP cache directory (defaults to $HOME/.vep/). Multiple plugins can be used by supplying the --plugin flag multiple times. See plugin documentation. Not used by default'),
ToolInput(
"help",
Boolean(optional=True),
prefix="--help",
doc="Display help message and quit",
),
ToolInput(
"quiet",
Boolean(optional=True),
prefix="--quiet",
doc="(-q) Suppress warning messages.Not used by default",
),
ToolInput(
"verbose",
Boolean(optional=True),
prefix="--verbose",
doc="(-v) Print out a bit more information while running. Not used by default",
),
ToolInput(
"config",
File(optional=True),
prefix="--config",
doc="""Load configuration options from a config file. The config file should consist of whitespace-separated pairs of option names and settings e.g.:
output_file my_output.txt
species mus_musculus
format vcf
host useastdb.ensembl.org
A config file can also be implicitly read; save the file as $HOME/.vep/vep.ini (or equivalent directory if
using --dir). Any options in this file will be overridden by those specified in a config file using --config,
and in turn by any options specified on the command line. You can create a quick version file of this by
setting the flags as normal and running VEP in verbose (-v) mode. This will output lines that can be copied
to a config file that can be loaded in on the next run using --config. Not used by default""",
),
ToolInput(
"everything",
Boolean(optional=True),
prefix="--everything",
doc="(-e) Shortcut flag to switch on all of the following: --sift b, --polyphen b, --ccds, "
"--uniprot, --hgvs, --symbol, --numbers, --domains, --regulatory, --canonical, --protein, "
"--biotype, --uniprot, --tsl, --appris, --gene_phenotype --af, --af_1kg, --af_esp, "
"--af_gnomad, --max_af, --pubmed, --variant_class, --mane",
),
ToolInput(
"species",
String(optional=True),
prefix="--species",
doc='Species for your data. This can be the latin name e.g. "homo_sapiens" or any Ensembl alias e.g. '
'"mouse". Specifying the latin name can speed up initial database connection as the registry does '
'not have to load all available database aliases on the server. Default = "homo_sapiens"',
),
ToolInput(
"assembly",
String(optional=True),
prefix="--assembly",
doc="""(-a) Select the assembly version to use if more than one available. If using the cache, you must
have the appropriate assembly's cache file installed. If not specified and you have only 1 assembly
version installed, this will be chosen by default. Default = use found assembly version""",
),
ToolInput(
"inputData",
String(optional=True),
prefix="--input_data",
doc="(--id) Raw input data as a string. May be used, for example, to input a single rsID or HGVS "
"notation quickly to vep: --input_data rs699",
),
ToolInput(
"format",
String(optional=True),
prefix="--format",
doc='Input file format - one of "ensembl", "vcf", "hgvs", "id", "region", "spdi". By default, '
"VEP auto-detects the input file format. Using this option you can specify the input file is "
"Ensembl, VCF, IDs, HGVS, SPDI or region format. Can use compressed version (gzipped) of any "
"file format listed above. Auto-detects format by default",
),
ToolInput(
"forceOverwrite",
Boolean(optional=True),
prefix="--force_overwrite",
doc="(--force) By default, VEP will fail with an error if the output file already exists. You can "
"force the overwrite of the existing file by using this flag. Not used by default",
),
ToolInput(
"statsFile",
String(optional=True),
default="variant_effect_output.txt_summary.html",
prefix="--stats_file",
doc="(--sf) Summary stats file name. This is an HTML file containing a summary of the VEP run - the "
'file name must end ".htm" or ".html". Default = "variant_effect_output.txt_summary.html"',
),
ToolInput(
"noStats",
Boolean(optional=True),
prefix="--no_stats",
doc="""Don\'t generate a stats file. Provides marginal gains in run time.""",
),
ToolInput(
"statsText",
Boolean(optional=True),
prefix="--stats_text",
doc="Generate a plain text stats file in place of the HTML.",
),
ToolInput(
"warningFile",
Filename(suffix="warning", extension=".txt"),
prefix="--warning_file",
doc="File name to write warnings and errors to. Default = STDERR (standard error)",
),
ToolInput(
"maxSvSize",
Boolean(optional=True),
prefix="--max_sv_size",
doc="Extend the maximum Structural Variant size VEP can process.",
),
ToolInput(
"noCheckVariantsOrder",
Boolean(optional=True),
prefix="--no_check_variants_order",
doc="Permit the use of unsorted input files. However running VEP on unsorted input files slows down "
"the tool and requires more memory.",
),
ToolInput(
"fork",
Int(optional=True),
default=CpuSelector(),
prefix="--fork",
doc="Enable forking, using the specified number of forks. Forking can dramatically improve runtime. "
"Not used by default",
),
ToolInput(
"custom",
Array(BedTabix, optional=True),
prefix="--custom",
prefix_applies_to_all_elements=True,
doc="Add custom annotation to the output. Files must be tabix indexed or in the bigWig format. "
"Multiple files can be specified by supplying the --custom flag multiple times. "
"See https://asia.ensembl.org/info/docs/tools/vep/script/vep_custom.html for full details. "
"Not used by default",
),
ToolInput(
"gff",
File(optional=True),
prefix="--gff",
doc="Use GFF transcript annotations in [filename] as an annotation source. "
"Requires a FASTA file of genomic sequence.Not used by default",
),
ToolInput(
"gtf",
File(optional=True),
prefix="--gtf",
doc="Use GTF transcript annotations in [filename] as an annotation source. "
"Requires a FASTA file of genomic sequence.Not used by default",
),
ToolInput(
"bam",
Bam(optional=True),
prefix="--bam",
doc="ADVANCED Use BAM file of sequence alignments to correct transcript models not derived from "
"reference genome sequence. Used to correct RefSeq transcript models. "
"Enables --use_transcript_ref; add --use_given_ref to override this behaviour. Not used by default",
),
ToolInput(
"useTranscriptRef",
Boolean(optional=True),
prefix="--use_transcript_ref",
doc="By default VEP uses the reference allele provided in the input file to calculate consequences "
"for the provided alternate allele(s). Use this flag to force VEP to replace the provided "
"reference allele with sequence derived from the overlapped transcript. This is especially "
"relevant when using the RefSeq cache, see documentation for more details. The GIVEN_REF and "
"USED_REF fields are set in the output to indicate any change. Not used by default",
),
ToolInput(
"useGivenRef",
Boolean(optional=True),
prefix="--use_given_ref",
doc="Using --bam or a BAM-edited RefSeq cache by default enables --use_transcript_ref; add this flag "
"to override this behaviour and use the provided reference allele from the input. Not used by default",
),
ToolInput(
"customMultiAllelic",
Boolean(optional=True),
prefix="--custom_multi_allelic",
doc="By default, comma separated lists found within the INFO field of custom annotation VCFs are "
"assumed to be allele specific. For example, a variant with allele_string A/G/C with associated "
'custom annotation "single,double,triple" will associate triple with C, double with G and single '
"with A. This flag instructs VEP to return all annotations for all alleles. Not used by default",
),
ToolInput(
"tab",
Boolean(optional=True),
prefix="--tab",
doc="Writes output in tab-delimited format. Not used by default",
),
ToolInput(
"json",
Boolean(optional=True),
prefix="--json",
doc="Writes output in JSON format. Not used by default",
),
ToolInput(
"compressOutput",
String(optional=True),
default="bgzip",
prefix="--compress_output",
doc="Writes output compressed using either gzip or bgzip. Not used by default",
),
ToolInput(
"fields",
Array(String, optional=True),
prefix="--fields",
doc="""Configure the output format using a comma separated list of fields.
Can only be used with tab (--tab) or VCF format (--vcf) output.
For the tab format output, the selected fields may be those present in the default output columns, or
any of those that appear in the Extra column (including those added by plugins or custom annotations).
Output remains tab-delimited. For the VCF format output, the selected fields are those present within the ""CSQ"" INFO field.
Example of command for the tab output:
--tab --fields ""Uploaded_variation,Location,Allele,Gene""
Example of command for the VCF format output:
--vcf --fields ""Allele,Consequence,Feature_type,Feature""
Not used by default""",
),
ToolInput(
"minimal",
Boolean(optional=True),
prefix="--minimal",
doc="Convert alleles to their most minimal representation before consequence calculation i.e. "
"sequence that is identical between each pair of reference and alternate alleles is trimmed "
"off from both ends, with coordinates adjusted accordingly. Note this may lead to discrepancies "
"between input coordinates and coordinates reported by VEP relative to transcript sequences; "
"to avoid issues, use --allele_number and/or ensure that your input variants have unique "
"identifiers. The MINIMISED flag is set in the VEP output where relevant. Not used by default",
),
ToolInput(
"variantClass",
Boolean(optional=True),
prefix="--variant_class",
doc="Output the Sequence Ontology variant class. Not used by default",
),
ToolInput(
"sift",
String(optional=True),
prefix="--sift",
doc="Species limited SIFT predicts whether an amino acid substitution affects protein function based "
"on sequence homology and the physical properties of amino acids. VEP can output the prediction "
"term, score or both. Not used by default",
),
ToolInput(
"polyphen",
String(optional=True),
prefix="--polyphen",
doc="Human only PolyPhen is a tool which predicts possible impact of an amino acid substitution on "
"the structure and function of a human protein using straightforward physical and comparative "
"considerations. VEP can output the prediction term, score or both. VEP uses the humVar score "
"by default - use --humdiv to retrieve the humDiv score. Not used by default",
),
ToolInput(
"humdiv",
Boolean(optional=True),
prefix="--humdiv",
doc="Human only Retrieve the humDiv PolyPhen prediction instead of the default humVar. "
"Not used by default",
),
ToolInput(
"nearest",
String(optional=True),
prefix="--nearest",
doc="""Retrieve the transcript or gene with the nearest protein-coding transcription start site
(TSS) to each input variant. Use ""transcript"" to retrieve the transcript stable ID, ""gene"" to
retrieve the gene stable ID, or ""symbol"" to retrieve the gene symbol. Note that the nearest
TSS may not belong to a transcript that overlaps the input variant, and more than one may be
reported in the case where two are equidistant from the input coordinates.
Currently only available when using a cache annotation source, and requires the Set::IntervalTree perl module.
Not used by default""",
),
ToolInput(
"distance",
Array(Int, optional=True),
separator=",",
prefix="--distance",
doc="Modify the distance up and/or downstream between a variant and a transcript for which VEP will assign the upstream_gene_variant or downstream_gene_variant consequences. Giving one distance will modify both up- and downstream distances; prodiving two separated by commas will set the up- (5') and down - (3') stream distances respectively. Default: 5000",
),
ToolInput(
"overlaps",
Boolean(optional=True),
prefix="--overlaps",
doc="Report the proportion and length of a transcript overlapped by a structural variant in VCF format.",
),
ToolInput(
"genePhenotype",
Boolean(optional=True),
prefix="--gene_phenotype",
doc="Indicates if the overlapped gene is associated with a phenotype, disease or trait. See list of phenotype sources. Not used by default",
),
ToolInput(
"regulatory",
Boolean(optional=True),
prefix="--regulatory",
doc="Look for overlaps with regulatory regions. VEP can also report if a variant falls in a high information position within a transcription factor binding site. Output lines have a Feature type of RegulatoryFeature or MotifFeature. Not used by default",
),
ToolInput(
"cellType",
Boolean(optional=True),
prefix="--cell_type",
doc="Report only regulatory regions that are found in the given cell type(s). Can be a single cell type or a comma-separated list. The functional type in each cell type is reported under CELL_TYPE in the output. To retrieve a list of cell types, use --cell_type list. Not used by default",
),
ToolInput(
"individual",
Array(String, optional=True),
prefix="--individual",
separator=",",
doc='Consider only alternate alleles present in the genotypes of the specified individual(s). May be a single individual, a comma-separated list or "all" to assess all individuals separately. Individual variant combinations homozygous for the given reference allele will not be reported. Each individual and variant combination is given on a separate line of output. Only works with VCF files containing individual genotype data; individual IDs are taken from column headers. Not used by default',
),
ToolInput(
"phased",
Boolean(optional=True),
prefix="--phased",
doc="Force VCF genotypes to be interpreted as phased. For use with plugins that depend on phased data. Not used by default",
),
ToolInput(
"alleleNumber",
Boolean(optional=True),
prefix="--allele_number",
doc="Identify allele number from VCF input, where 1 = first ALT allele, 2 = second ALT allele etc. Useful when using --minimal Not used by default",
),
ToolInput(
"showRefAllele",
Boolean(optional=True),
prefix="--show_ref_allele",
doc='Adds the reference allele in the output. Mainly useful for the VEP "default" and tab-delimited output formats. Not used by default',
),
ToolInput(
"totalLength",
Boolean(optional=True),
prefix="--total_length",
doc="Give cDNA, CDS and protein positions as Position/Length. Not used by default",
),
ToolInput(
"numbers",
Boolean(optional=True),
prefix="--numbers",
doc="Adds affected exon and intron numbering to to output. Format is Number/Total. Not used by default",
),
ToolInput(
"noEscape",
Boolean(optional=True),
prefix="--no_escape",
doc="Don't URI escape HGVS strings. Default = escape",
),
ToolInput(
"keepCsq",
Boolean(optional=True),
prefix="--keep_csq",
doc="Don't overwrite existing CSQ entry in VCF INFO field. Overwrites by default",
),
ToolInput(
"vcfInfoField",
String(optional=True),
prefix="--vcf_info_field",
doc='Change the name of the INFO key that VEP write the consequences to in its VCF output. Use "ANN" for compatibility with other tools such as snpEff. Default: CSQ',
),
ToolInput(
"terms",
String(optional=True),
prefix="--terms",
doc='(-t) The type of consequence terms to output. The Ensembl terms are described here. The Sequence Ontology is a joint effort by genome annotation centres to standardise descriptions of biological sequences. Default = "SO"',
),
ToolInput(
"noHeaders",
Boolean(optional=True),
prefix="--no_headers",
doc="Don't write header lines in output files. Default = add headers",
),
ToolInput(
"hgvs",
Boolean(optional=True),
prefix="--hgvs",
doc="Add HGVS nomenclature based on Ensembl stable identifiers to the output. Both coding and protein sequence names are added where appropriate. To generate HGVS identifiers when using --cache or --offline you must use a FASTA file and --fasta. HGVS notations given on Ensembl identifiers are versioned. Not used by default",
),
ToolInput(
"hgvsg",
Boolean(optional=True),
prefix="--hgvsg",
doc="Add genomic HGVS nomenclature based on the input chromosome name. To generate HGVS identifiers when using --cache or --offline you must use a FASTA file and --fasta. Not used by default",
),
ToolInput(
"shiftHgvs",
Boolean(optional=True),
prefix="--shift_hgvs",
doc="""Enable or disable 3\' shifting of HGVS notations. When enabled, this causes ambiguous insertions or deletions (typically in repetetive sequence tracts) to be "shifted" to their most 3' possible coordinates (relative to the transcript sequence and strand) before the HGVS notations are calculated; the flag HGVS_OFFSET is set to the number of bases by which the variant has shifted, relative to the input genomic coordinates. Disabling retains the original input coordinates of the variant. Default: 1 (shift)""",
),
ToolInput(
"transcriptVersion",
Boolean(optional=True),
prefix="--transcript_version",
doc="Add version numbers to Ensembl transcript identifiers",
),
ToolInput(
"protein",
Boolean(optional=True),
prefix="--protein",
doc="Add the Ensembl protein identifier to the output where appropriate. Not used by default",
),
ToolInput(
"symbol",
Boolean(optional=True),
prefix="--symbol",
doc="Adds the gene symbol (e.g. HGNC) (where available) to the output. Not used by default",
),
ToolInput(
"ccds",
Boolean(optional=True),
prefix="--ccds",
doc="Adds the CCDS transcript identifer (where available) to the output. Not used by default",
),
ToolInput(
"uniprot",
Boolean(optional=True),
prefix="--uniprot",
doc="Adds best match accessions for translated protein products from three UniProt-related databases (SWISSPROT, TREMBL and UniParc) to the output. Not used by default",
),
ToolInput(
"tsl",
Boolean(optional=True),
prefix="--tsl",
doc="Adds the transcript support level for this transcript to the output. Not used by default. Note: Only available for human on the GRCh38 assembly",
),
ToolInput(
"appris",
Boolean(optional=True),
prefix="--appris",
doc="Adds the APPRIS isoform annotation for this transcript to the output. Not used by default. Note: Only available for human on the GRCh38 assembly",
),
ToolInput(
"canonical",
Boolean(optional=True),
prefix="--canonical",
doc="Adds a flag indicating if the transcript is the canonical transcript for the gene. Not used by default",
),
ToolInput(
"mane",
Boolean(optional=True),
prefix="--mane",
doc="Adds a flag indicating if the transcript is the MANE Select transcript for the gene. Not used by default. Note: Only available for human on the GRCh38 assembly",
),
ToolInput(
"biotype",
Boolean(optional=True),
prefix="--biotype",
doc="Adds the biotype of the transcript or regulatory feature. Not used by default",
),
ToolInput(
"domains",
Boolean(optional=True),
prefix="--domains",
doc="Adds names of overlapping protein domains to output. Not used by default",
),
ToolInput(
"xrefRefseq",
Boolean(optional=True),
prefix="--xref_refseq",
doc="Output aligned RefSeq mRNA identifier for transcript. Not used by default. Note: The RefSeq and Ensembl transcripts aligned in this way MAY NOT, AND FREQUENTLY WILL NOT, match exactly in sequence, exon structure and protein product",
),
ToolInput(
"synonyms",
Tsv(optional=True),
prefix="--synonyms",
doc="Load a file of chromosome synonyms. File should be tab-delimited with the primary identifier in column 1 and the synonym in column 2. Synonyms allow different chromosome identifiers to be used in the input file and any annotation source (cache, database, GFF, custom file, FASTA file). Not used by default",
),
ToolInput(
"checkExisting",
Boolean(optional=True),
prefix="--check_existing",
doc="""Checks for the existence of known variants that are co-located with your input. By default the alleles are compared and variants on an allele-specific basis - to compare only coordinates, use --no_check_alleles.
Some databases may contain variants with unknown (null) alleles and these are included by default; to exclude them use --exclude_null_alleles.
See this page for more details.
Not used by default""",
),
ToolInput(
"checkSvs",
Boolean(optional=True),
prefix="--check_svs",
doc="Checks for the existence of structural variants that overlap your input. Currently requires database access. Not used by default",
),
ToolInput(
"clinSigAllele",
Boolean(optional=True),
prefix="--clin_sig_allele",
doc="Return allele specific clinical significance. Setting this option to 0 will provide all known clinical significance values at the given locus. Default: 1 (Provide allele-specific annotations)",
),
ToolInput(
"excludeNullAlleles",
Boolean(optional=True),
prefix="--exclude_null_alleles",
doc="Do not include variants with unknown alleles when checking for co-located variants. Our human database contains variants from HGMD and COSMIC for which the alleles are not publically available; by default these are included when using --check_existing, use this flag to exclude them. Not used by default",
),
ToolInput(
"noCheckAlleles",
Boolean(optional=True),
prefix="--no_check_alleles",
doc="""When checking for existing variants, by default VEP only reports a co-located variant if none of the input alleles are novel. For example, if your input variant has alleles A/G, and an existing co-located variant has alleles A/C, the co-located variant will not be reported.
Strand is also taken into account - in the same example, if the input variant has alleles T/G but on the negative strand, then the co-located variant will be reported since its alleles match the reverse complement of input variant.
Use this flag to disable this behaviour and compare using coordinates alone. Not used by default""",
),
ToolInput(
"af",
Boolean(optional=True),
prefix="--af",
doc="Add the global allele frequency (AF) from 1000 Genomes Phase 3 data for any known co-located variant to the output. For this and all --af_* flags, the frequency reported is for the input allele only, not necessarily the non-reference or derived allele. Not used by default",
),
ToolInput(
"maxAf",
Boolean(optional=True),
prefix="--max_af",
doc="Report the highest allele frequency observed in any population from 1000 genomes, ESP or gnomAD. Not used by default",
),
ToolInput(
"af1kg",
String(optional=True),
prefix="--af_1kg",
doc="Add allele frequency from continental populations (AFR,AMR,EAS,EUR,SAS) of 1000 Genomes Phase 3 to the output. Must be used with --cache. Not used by default",
),
ToolInput(
"afEsp",
Boolean(optional=True),
prefix="--af_esp",
doc="Include allele frequency from NHLBI-ESP populations. Must be used with --cache. Not used by default",
),
ToolInput(
"afGnomad",
Boolean(optional=True),
prefix="--af_gnomad",
doc="Include allele frequency from Genome Aggregation Database (gnomAD) exome populations. Note only data from the gnomAD exomes are included; to retrieve data from the additional genomes data set, see this guide. Must be used with --cache Not used by default",
),
ToolInput(
"afExac",
Boolean(optional=True),
prefix="--af_exac",
doc="Include allele frequency from ExAC project populations. Must be used with --cache. Not used by default. Note: ExAC data has been superceded by gnomAD. This flag remains for those wishing to use older cache versions containing ExAC data.",
),
ToolInput(
"pubmed",
Boolean(optional=True),
prefix="--pubmed",
doc="Report Pubmed IDs for publications that cite existing variant. Must be used with --cache. Not used by default",
),
ToolInput(
"failed",
Boolean(optional=True),
prefix="--failed",
doc="When checking for co-located variants, by default VEP will exclude variants that have been flagged as failed. Set this flag to include such variants. Default: 0 (exclude)",
),
ToolInput(
"gencodeBasic",
Boolean(optional=True),
prefix="--gencode_basic",
doc="Limit your analysis to transcripts belonging to the GENCODE basic set. This set has fragmented or problematic transcripts removed. Not used by default",
),
ToolInput(
"excludePredicted",
Boolean(optional=True),
prefix="--exclude_predicted",
doc='When using the RefSeq or merged cache, exclude predicted transcripts (i.e. those with identifiers beginning with "XM_" or "XR_").',
),
ToolInput(
"transcriptFilter",
Boolean(optional=True),
prefix="--transcript_filter",
doc='''ADVANCED Filter transcripts according to any arbitrary set of rules. Uses similar notation to filter_vep.
You may filter on any key defined in the root of the transcript object; most commonly this will be ""stable_id"":
--transcript_filter ""stable_id match N[MR]_""''',
),
ToolInput(
"checkRef",
Boolean(optional=True),
prefix="--check_ref",
doc="Force VEP to check the supplied reference allele against the sequence stored in the Ensembl Core database or supplied FASTA file. Lines that do not match are skipped. Not used by default",
),
ToolInput(
"lookupRef",
Boolean(optional=True),
prefix="--lookup_ref",
doc="Force overwrite the supplied reference allele with the sequence stored in the Ensembl Core database or supplied FASTA file. Not used by default",
),
ToolInput(
"dontSkip",
Boolean(optional=True),
prefix="--dont_skip",
doc="Don't skip input variants that fail validation, e.g. those that fall on unrecognised sequences. Combining --check_ref with --dont_skip will add a CHECK_REF output field when the given reference does not match the underlying reference sequence.",
),
ToolInput(
"allowNonVariant",
Boolean(optional=True),
prefix="--allow_non_variant",
doc="When using VCF format as input and output, by default VEP will skip non-variant lines of input (where the ALT allele is null). Enabling this option the lines will be printed in the VCF output with no consequence data added.",
),
ToolInput(
"chr",
Array(String, optional=True),
prefix="--chr",
separator=",",
doc='Select a subset of chromosomes to analyse from your file. Any data not on this chromosome in the input will be skipped. The list can be comma separated, with "-" characters representing an interval. For example, to include chromosomes 1, 2, 3, 10 and X you could use --chr 1-3,10,X Not used by default',
),
ToolInput(
"codingOnly",
Boolean(optional=True),
prefix="--coding_only",
doc="Only return consequences that fall in the coding regions of transcripts. Not used by default",
),
ToolInput(
"noIntergenic",
Boolean(optional=True),
prefix="--no_intergenic",
doc="Do not include intergenic consequences in the output. Not used by default",
),
ToolInput(
"pick",
Boolean(optional=True),
prefix="--pick",
doc="Pick once line or block of consequence data per variant, including transcript-specific columns. Consequences are chosen according to the criteria described here, and the order the criteria are applied may be customised with --pick_order. This is the best method to use if you are interested only in one consequence per variant. Not used by default",
),
ToolInput(
"pickAllele",
Boolean(optional=True),
prefix="--pick_allele",
doc="Like --pick, but chooses one line or block of consequence data per variant allele. Will only differ in behaviour from --pick when the input variant has multiple alternate alleles. Not used by default",
),
ToolInput(
"perGene",
Boolean(optional=True),
prefix="--per_gene",
doc="Output only the most severe consequence per gene. The transcript selected is arbitrary if more than one has the same predicted consequence. Uses the same ranking system as --pick. Not used by default",
),
ToolInput(
"pickAlleleGene",
Boolean(optional=True),
prefix="--pick_allele_gene",
doc="Like --pick_allele, but chooses one line or block of consequence data per variant allele and gene combination. Not used by default",
),
ToolInput(
"flagPick",
Boolean(optional=True),
prefix="--flag_pick",
doc="As per --pick, but adds the PICK flag to the chosen block of consequence data and retains others. Not used by default",
),
ToolInput(
"flagPickAllele",
Boolean(optional=True),
prefix="--flag_pick_allele",
doc="As per --pick_allele, but adds the PICK flag to the chosen block of consequence data and retains others. Not used by default",
),
ToolInput(
"flagPickAlleleGene",
Boolean(optional=True),
prefix="--flag_pick_allele_gene",
doc="As per --pick_allele_gene, but adds the PICK flag to the chosen block of consequence data and retains others. Not used by default",
),
ToolInput(
"pickOrder",
Array(String, optional=True),
prefix="--pick_order",
separator=",",
doc="""Customise the order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: --pick, --pick_allele, --per_gene, --pick_allele_gene, --flag_pick, --flag_pick_allele, --flag_pick_allele_gene. See this page for the default order.
Valid criteria are: [ canonical appris tsl biotype ccds rank length mane ]. e.g.:
--pick --pick_order tsl,appris,rank""",
),
ToolInput(
"mostSevere",
Boolean(optional=True),
prefix="--most_severe",
doc="Output only the most severe consequence per variant. Transcript-specific columns will be left blank. Consequence ranks are given in this table. To include regulatory consequences, use the --regulatory option in combination with this flag. Not used by default",
),
ToolInput(
"summary",
Boolean(optional=True),
prefix="--summary",
doc="Output only a comma-separated list of all observed consequences per variant. Transcript-specific columns will be left blank. Not used by default",
),
ToolInput(
"filterCommon",
Boolean(optional=True),
prefix="--filter_common",
doc="Shortcut flag for the filters below - this will exclude variants that have a co-located existing variant with global AF > 0.01 (1%). May be modified using any of the following freq_* filters. Not used by default",
),
ToolInput(
"checkFrequency",
Boolean(optional=True),
prefix="--check_frequency",
doc="Turns on frequency filtering. Use this to include or exclude variants based on the frequency of co-located existing variants in the Ensembl Variation database. You must also specify all of the --freq_* flags below. Frequencies used in filtering are added to the output under the FREQS key in the Extra field. Not used by default",
),
ToolInput(
"freqPop",
String(optional=True),
prefix="--freq_pop",
doc="Name of the population to use in frequency filter. This must be one of the following: (1KG_ALL, 1KG_AFR, 1KG_AMR, 1KG_EAS, 1KG_EUR, 1KG_SAS, AA, EA, gnomAD, gnomAD_AFR, gnomAD_AMR, gnomAD_ASJ, gnomAD_EAS, gnomAD_FIN, gnomAD_NFE, gnomAD_OTH, gnomAD_SAS)",
),
ToolInput(
"freqFreq",
Float(optional=True),
prefix="--freq_freq",
doc="Allele frequency to use for filtering. Must be a float value between 0 and 1",
),
ToolInput(
"freqGtLt",
String(optional=True),
prefix="--freq_gt_lt",
doc="Specify whether the frequency of the co-located variant must be greater than (gt) or less than (lt) the value specified with --freq_freq",
),
ToolInput(
"freqFilter",
String(optional=True),
prefix="--freq_filter",
doc="Specify whether to exclude or include only variants that pass the frequency filter",
),
# CADD plugin
ToolInput("caddReference", Array(VcfTabix, optional=True)),
# Condel
ToolInput(
"condelConfig",
Directory(optional=True),
doc="Directory containing CondelPlugin config, in format: '<dir>/condel_SP.conf'",
),
# dbNSFP
ToolInput("dbnspReference", VcfTabix(optional=True), doc=""),
ToolInput("dbsnpColumns", Array(String, optional=True)),
# REVEL
ToolInput("revelReference", VcfTabix(optional=True)),
# CUSTOM
ToolInput("custom1Reference", VcfTabix(optional=True)),
ToolInput("custom1Columns", Array(String, optional=True)),
ToolInput("custom2Reference", VcfTabix(optional=True)),
ToolInput("custom2Columns", Array(String, optional=True)),
]
def inputs(self) -> List[ToolInput]:
return [
ToolInput("piscesVersion", String()),
ToolInput(
"inputBam",
BamBai(),
prefix="-b",
position=4,
shell_quote=False,
doc="Input BAM file",
),
ToolInput(
"referenceFolder",
Directory(),
prefix="--genomefolders",
position=5,
shell_quote=False,
doc="Folder containing reference genome files",
),
ToolInput(
"outputDir",
String(),
prefix="--outfolder",
position=4,
shell_quote=False,
doc="Output directory",
),
ToolInput(
"intervalBedFile",
Bed(optional=True),
prefix="-i",
position=5,
shell_quote=False,
doc="Bed File denoting regions to call variants.",
),
ToolInput(
"minimumBaseQuality",
Int(optional=True),
prefix="--minbq",
position=5,
shell_quote=False,
default=20,
doc="Minimum base call quality to use base in read. (Default: 20)",
),
ToolInput(
"callMNVs",
String(optional=True),
prefix="--callmnvs",
position=5,
shell_quote=False,
doc="Call Multi Nucleotide Variants (aka Phased SNPs). (Default: false)",
),
ToolInput(
"outputSBFiles",
String(optional=True),
prefix="--outputsbfiles",
position=5,
shell_quote=False,
doc="Boolean Flag to output strand bias files. (Default: false)",
),
*self.pisces_additional_args,
]
def inputs(self):
return [
ToolInput(
tag="run",
input_type=Directory(),
prefix="--run=",
separate_value_from_prefix=False,
doc="Path of Illumina BCL run folder.",
),
ToolInput(
tag="id",
input_type=String(optional=True),
prefix="--id=",
separate_value_from_prefix=False,
doc="Name of the folder created by mkfastq. If not supplied, will default to the name of the flowcell referred to by the --run argument.",
),
ToolInput(
tag="outputFoldername",
input_type=Filename(),
prefix="--output-dir=",
separate_value_from_prefix=False,
doc="Same as in bcl2fastq. Folder where FASTQs, reports and stats will be generated.",
),
ToolInput(
tag="csv",
input_type=Csv(optional=True),
prefix="--csv=",
separate_value_from_prefix=False,
doc="Apparently the same as `sampleSheet`. The sample sheet can either be a simple CSV with lane, sample and index columns, or an Illumina Experiment Manager-compatible sample sheet. Sample sheet indexes can refer to 10x sample index set names (e.g., SI-GA-A12).",
),
ToolInput(
tag="sampleSheet",
input_type=File(optional=True),
prefix="--sample-sheet=",
separate_value_from_prefix=False,
doc="(--samplesheet= | --csv=) Path to the sample sheet. The sample sheet can either be a simple CSV with lane, sample and index columns, or an Illumina Experiment Manager-compatible sample sheet. Sample sheet indexes can refer to 10x sample index set names (e.g., SI-GA-A12).",
),
ToolInput(
tag="ignoreDualIndex",
input_type=Boolean(optional=True),
prefix="--ignore-dual-index",
separate_value_from_prefix=True,
doc="On a dual-indexed flowcell, ignore the second sample index, if the second sample index was not used for the 10x sample.",
),
ToolInput(
tag="qc",
input_type=Boolean(optional=True),
prefix="--qc",
separate_value_from_prefix=True,
doc="Calculate both sequencing and 10x-specific metrics, including per-sample barcode matching rate. Will not be performed unless this flag is specified.",
),
ToolInput(
tag="lanes",
input_type=Array(String, optional=True),
prefix="--lanes=",
separate_value_from_prefix=False,
separator=",",
doc="Comma-delimited series of lanes to demultiplex. Shortcut for the --tiles argument.",
),
ToolInput(
tag="useBasesMask",
input_type=String(optional=True),
prefix="--use-bases-mask=",
separate_value_from_prefix=False,
doc="Same as bcl2fastq; override the read lengths as specified in RunInfo.xml. See Illumina bcl2fastq documentation for more information.",
),
ToolInput(
tag="deleteUndetermined",
input_type=Boolean(optional=True),
prefix="--delete-undetermined",
separate_value_from_prefix=True,
doc="Delete the Undetermined FASTQ files left by bcl2fastq. Useful if your sample sheet is only expected to match a subset of the flowcell.",
),
ToolInput(
tag="project",
input_type=String(optional=True),
prefix="--project=",
separate_value_from_prefix=False,
doc="Custom project name, to override the samplesheet or to use in conjunction with the --csv argument.",
),
# mfranklin: These are only supported in cluster modes which I've disabled
# ToolInput(
# tag="jobmode",
# input_type=String(optional=True),
# prefix="--jobmode=",
# separate_value_from_prefix=False,
# doc="Job manager to use. Valid options: local (default), sge, lsf, or a .template file",
# ),
# ToolInput(
# tag="mempercore",
# input_type=String(optional=True),
# prefix="--mempercore=",
# separate_value_from_prefix=False,
# doc="Set max GB each job may use at one time. Only applies in cluster jobmodes.",
# ),
# ToolInput(
# tag="maxjobs",
# input_type=String(optional=True),
# prefix="--maxjobs=",
# separate_value_from_prefix=False,
# doc="Set max jobs submitted to cluster at one time. Only applies in cluster jobmodes.",
# ),
# ToolInput(
# tag="jobinterval",
# input_type=String(optional=True),
# prefix="--jobinterval=",
# separate_value_from_prefix=False,
# doc="Set delay between submitting jobs to cluster, in ms. Only applies in cluster jobmodes.",
# ),
# ToolInput(
# tag="overrides",
# input_type=File(optional=True),
# prefix="--overrides=",
# separate_value_from_prefix=False,
# doc="The path to a JSON file that specifies stage-level overrides for cores and memory. Finer-grained than --localcores, --mempercore and --localmem. Consult the 10x support website for an example override file.",
# ),
ToolInput(
tag="localcores",
input_type=Int(optional=True),
default=CpuSelector(),
prefix="--localcores=",
separate_value_from_prefix=False,
doc="Set max cores the pipeline may request at one time. Only applies when --jobmode=local.",
),
ToolInput(
tag="localmem",
input_type=Float(optional=True),
default=MemorySelector(),
prefix="--localmem=",
separate_value_from_prefix=False,
doc="Set max GB the pipeline may request at one time. Only applies when --jobmode=local.",
),
# ToolInput(
# tag="uiport",
# input_type=Boolean(optional=True),
# prefix="--uiport=",
# separate_value_from_prefix=False,
# doc="Serve web UI at http://localhost:PORT",
# ),
# ToolInput(
# tag="disableUi",
# input_type=String(optional=True),
# prefix="--disable-ui",
# separate_value_from_prefix=True,
# doc="Do not serve the UI.",
# ),
# ToolInput(
# tag="noexit",
# input_type=String(optional=True),
# prefix="--noexit",
# separate_value_from_prefix=True,
# doc="Keep web UI running after pipestance completes or fails.",
# ),
ToolInput(
tag="nopreflight",
input_type=Boolean(optional=True),
prefix="--nopreflight",
separate_value_from_prefix=True,
doc="Skip preflight checks.",
),
# ToolInput(
# tag="help",
# input_type=String(optional=True),
# prefix="-h",
# separate_value_from_prefix=True,
# doc="Show this message.",
# ),
# ToolInput(
# tag="version",
# input_type=String(optional=True),
# prefix="--version",
# separate_value_from_prefix=True,
# doc="Show version.",
# ),
]
def constructor(self):
##INPUTS
self.input("bam", BamBai())
self.input("sample_name", String())
self.input("reference_folder", Directory())
self.input("intervals", Bed())
self.input("gemini_chromosomes", String(optional=True))
self.input("ploidy", String(optional=True), default="somatic")
self.input("min_bq", Int(optional=True))
self.input("min_mq", Int(optional=True))
self.input("min_dp", Int(optional=True))
self.input("min_vaf", Float(optional=True))
self.input("vc_min_vq", Int(optional=True))
self.input("noise_level", Int(optional=True))
self.input("vqr_min_vq", Int(optional=True))
self.input("pisces_awk_script", File())
## STEPS
self.step(
"primary_only",
SamToolsView_1_9(sam=self.bam,
doNotOutputAlignmentsWithBitsSet="0x100"),
)
self.step(
"index_primary_only_bam",
SamToolsIndex_1_9(bam=self.primary_only.out),
)
self.step(
"gemini_read_preprocessing",
PiscesGemini_5_3_0_0(
inputBam=self.index_primary_only_bam,
referenceFolder=self.reference_folder,
samtoolsExecutable="samtools",
chromosomeFilter=self.gemini_chromosomes,
outputDir=".",
piscesVersion="5.3.0.0",
),
)
self.step(
"pisces",
PiscesVariantCaller_5_3_0_0(
inputBam=self.gemini_read_preprocessing.bam,
referenceFolder=self.reference_folder,
outputDir=".",
intervalBedFile=self.intervals,
ploidy=self.ploidy,
minimumBaseQuality=self.min_bq,
minimumMappingQuality=self.min_mq,
minimumVariantFrequency=self.min_vaf,
noiseLevelForQModel=self.noise_level,
minimumVariantFrequencyFilter=self.min_vaf,
enableSingleStrandFilter="True",
outputSBFiles="True",
callMNVs="False",
maxMNVLength=1,
RMxNFilter="5,9,0.35",
variantQualityFilter=self.vc_min_vq,
crushVCF="False",
gVCF="False",
piscesVersion="5.3.0.0",
),
)
self.step(
"vqr",
PiscesVariantQualityRecalibration_5_3_0_0(
inputVcf=self.pisces.vcf,
outputDir=".",
baselineNoise=self.noise_level,
minVariantQuality=self.vqr_min_vq,
piscesVersion="5.3.0.0",
),
)
piscesVcf = FirstOperator([self.vqr.vcf, self.pisces.vcf])
self.step(
"fixSource",
Awk(script=self.pisces_awk_script, input_files=piscesVcf),
)
self.step("sort", BcfToolsSort_1_9(vcf=self.fixSource.out))
self.step("normalise", BcfToolsNorm_1_9(vcf=self.sort.out))
self.step("uncompress", UncompressArchive(file=self.normalise.out))
self.step(
"filterpass",
VcfToolsvcftools_0_1_16(
vcf=self.uncompress.out.as_type(Vcf),
removeFileteredAll=True,
recode=True,
recodeINFOAll=True,
),
)
## OUTPUTS
self.output("variants", source=self.sort.out)
self.output("out", source=self.filterpass.out)
self.output("out_bam", source=self.gemini_read_preprocessing.bam)
def inputs(self):
return [
*super().inputs(), # cache options
ToolInput(
"cache",
Boolean(optional=True),
default=True,
prefix="--cache",
doc=
"Enables use of the cache. Add --refseq or --merged to use the refseq or merged cache.",
),
ToolInput(
"cacheDir",
Directory(optional=True),
prefix="--dir",
doc=
'Specify the base cache/plugin directory to use. Default = "$HOME/.vep/"',
),
ToolInput(
"dirCache",
Directory(optional=True),
prefix="--dir_cache",
doc=
'Specify the cache directory to use. Default = "$HOME/.vep/"',
),
ToolInput(
"dirPlugins",
Directory(optional=True),
prefix="--dir_plugins",
doc=
'Specify the plugin directory to use. Default = "$HOME/.vep/"',
),
ToolInput(
"offline",
Boolean(optional=True),
default=True,
prefix="--offline",
doc=
"Enable offline mode. No database connections will be made, and a cache file or GFF/GTF file is "
"required for annotation. Add --refseq to use the refseq cache (if installed). Not used by default",
),
ToolInput(
"fasta",
FastaWithDict(optional=True),
prefix="--fasta",
doc=
"(--fa) Specify a FASTA file or a directory containing FASTA files to use to look up reference "
"sequence. The first time you run VEP with this parameter an index will be built which can take a "
"few minutes. This is required if fetching HGVS annotations (--hgvs) or checking reference "
"sequences (--check_ref) in offline mode (--offline), and optional with some performance increase "
"in cache mode (--cache). See documentation for more details. Not used by default",
),
ToolInput(
"refseq",
Boolean(optional=True),
prefix="--refseq",
doc=
"Specify this option if you have installed the RefSeq cache in order for VEP to pick up the "
"alternate cache directory. This cache contains transcript objects corresponding to RefSeq "
"transcripts. Consequence output will be given relative to these transcripts in place of the "
"default Ensembl transcripts (see documentation)",
),
ToolInput(
"merged",
Boolean(optional=True),
prefix="--merged",
doc=
"Use the merged Ensembl and RefSeq cache. Consequences are flagged "
"with the SOURCE of each transcript used.",
),
ToolInput(
"cacheVersion",
Boolean(optional=True),
prefix="--cache_version",
doc=
"Use a different cache version than the assumed default (the VEP version). This should be used "
"with Ensembl Genomes caches since their version numbers do not match Ensembl versions. "
"For example, the VEP/Ensembl version may be 88 and the Ensembl Genomes version 35. "
"Not used by default",
),
ToolInput(
"showCacheInfo",
Boolean(optional=True),
prefix="--show_cache_info",
doc=
"Show source version information for selected cache and quit",
),
ToolInput(
"bufferSize",
Int(optional=True),
prefix="--buffer_size",
doc=
"Sets the internal buffer size, corresponding to the number of variants that are read in to memory "
"simultaneously. Set this lower to use less memory at the expense of longer run time, and higher "
"to use more memory with a faster run time. Default = 5000",
),
]
def constructor(self):
## INPUTS
self.input("bam", BamBai())
self.input("sample_name", String())
self.input("reference_folder", Directory())
self.input("intervals", Bed())
self.input("ploidy", String(optional=True), default="somatic")
self.input("min_bq", Int(optional=True))
self.input("min_mq", Int(optional=True))
self.input("min_dp", Int(optional=True), default=100)
self.input("min_vaf", Float(optional=True))
self.input("vc_min_vq", Int(optional=True))
self.input("noise_level", Int(optional=True))
self.input("vqr_min_vq", Int(optional=True))
self.input("pisces_awk_script", File())
## STEPS
self.step(
"primary_only",
SamToolsView_1_9(sam=self.bam,
doNotOutputAlignmentsWithBitsSet="0x100"),
)
self.step(
"index_primary_only_bam",
SamToolsIndex_1_9(bam=self.primary_only.out),
)
self.step(
"hygea_realignment",
PiscesHygeaRealigner_5_2_10_49(
inputBam=self.index_primary_only_bam,
outputDir=".",
referenceFolder=self.reference_folder,
skipAndRemoveDuplicates="true",
piscesVersion="5.2.10.49",
),
)
self.step(
"stitcher_read_joining",
PiscesStitcher_5_2_10_49(
inputBam=self.hygea_realignment.out,
outputDir=".",
sampleName=self.sample_name,
piscesVersion="5.2.10.49",
),
)
self.step(
"stitcher_sort",
SamToolsSort_1_9(
bam=self.stitcher_read_joining.out,
outputFilename=self.sample_name + ".bam",
),
)
self.step("stitcher_index",
SamToolsIndex_1_9(bam=self.stitcher_sort.out))
self.step(
"pisces",
PiscesVariantCaller_5_2_10_49(
inputBam=self.stitcher_index.out,
referenceFolder=self.reference_folder,
outputDir=".",
intervalBedFile=self.intervals,
ploidy=self.ploidy,
minimumBaseQuality=self.min_bq,
minimumMappingQuality=self.min_mq,
minimumVariantFrequency=self.min_vaf,
minimumCoverage=self.min_dp,
noiseLevelForQModel=self.noise_level,
minimumVariantFrequencyFilter=self.min_vaf,
enableSingleStrandFilter="true",
callMNVs="false",
maxMNVLength=1,
RMxNFilter="5,9,0.35",
variantQualityFilter=self.vc_min_vq,
crushVCF="false",
gVCF="false",
piscesVersion="5.2.10.49",
),
)
self.step(
"vqr",
PiscesVariantQualityRecalibration_5_2_10_49(
inputVcf=self.pisces.vcf,
outputDir=".",
baselineNoise=self.noise_level,
minVariantQuality=self.vqr_min_vq,
piscesVersion="5.2.10.49",
),
)
piscesVcf = FirstOperator([self.vqr.vcf, self.pisces.vcf])
self.step(
"fixSource",
Awk(script=self.pisces_awk_script, input_files=piscesVcf),
)
self.step("sort", BcfToolsSort_1_9(vcf=self.fixSource.out))
self.step("normalise", BcfToolsNorm_1_9(vcf=self.sort.out))
self.step("uncompress", UncompressArchive(file=self.normalise.out))
self.step(
"filterpass",
VcfToolsvcftools_0_1_16(
vcf=self.uncompress.out.as_type(Vcf),
removeFileteredAll=True,
recode=True,
recodeINFOAll=True,
),
)
## OUTPUTs
self.output("variants", source=self.sort.out)
self.output("out", source=self.filterpass.out)
self.output("out_bam", source=self.stitcher_index.out)
## OPTIONAL OUTPUTs
self.output("hygea_options",
source=self.hygea_realignment.used_options)
self.output("stitcher_options",
source=self.stitcher_read_joining.used_options)
self.output("pisces_options", source=self.pisces.used_options)
self.output("vqr_options", source=self.vqr.used_options)
class Gatk4VariantAnnotatorBase(Gatk4ToolBase):
@classmethod
def gatk_command(cls):
return "VariantAnnotator"
def tool(self) -> str:
return "Gatk4VariantAnnotator"
def friendly_name(self) -> str:
return "GATK4: VariantAnnotator(BETA)"
def inputs(self):
return [
*super().inputs(),
ToolInput(
"reference",
FastaWithIndexes(),
prefix="--reference",
position=2,
shell_quote=False,
doc="Reference Genome FASTA",
),
ToolInput(
"inputBam",
BamBai(),
prefix="--input",
position=2,
shell_quote=False,
doc="Input BAM",
),
ToolInput(
"inputVcf",
Vcf(),
prefix="--variant",
position=2,
shell_quote=False,
doc="Input VCF",
),
ToolInput(
"outputVcf",
Filename(),
prefix="--output",
position=2,
shell_quote=False,
doc="Output VCF filename",
),
*self.additional_variant_annotator_args,
]
def outputs(self):
return [ToolOutput("out", Vcf(), selector=InputSelector("outputVcf"))]
def bind_metadata(self):
return ToolMetadata(
contributors=["Miriam M Yeung"],
dateCreated=datetime(2021, 9, 13),
dateUpdated=datetime(2021, 9, 13),
documentation=
"USAGE: VariantAnnotator [arguments]\nAnnotate variant calls based on their context information",
)
additional_variant_annotator_args = [
## Input modifiers
ToolInput(
"readIndex",
String(optional=True),
prefix="--read-index",
position=3,
shell_quote=False,
doc=
"Index for BAM, if not provided the path to the index is inferred. [Default: none]",
),
ToolInput(
"readValidationStringency",
String(optional=True),
prefix="--read-validation-stringency",
position=3,
shell_quote=False,
doc=
"Validation stringency for BAM files, the default value (SILENT) can improve performance when the BAM file contains variable-length data (read,qualities, tags) do not need to be decoded. [Default: SILENT]\nValid inputs: SILENT | LENIENT | STRICT",
),
## Annotations
ToolInput(
"annotation",
String(optional=True),
prefix="-annotation",
position=3,
shell_quote=False,
doc=
"Which annotations to include in variant calls in the output. These supplement annotations provided by annotation groups.\nSee https://gatk.broadinstitute.org/hc/en-us/articles/4405443524763--Tool-Documentation-Index#VariantAnnotations for valid options",
),
ToolInput(
"annotationGroup",
String(optional=True),
prefix="--annotation-group",
position=3,
shell_quote=False,
doc=
"Which groups of annotations to add to the output variant calls. Any requirements that are not met (e.g. failing to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.\nSee https://gatk.broadinstitute.org/hc/en-us/articles/4405443524763--Tool-Documentation-Index#VariantAnnotations for valid options",
),
ToolInput(
"annotationsExclude",
String(optional=True),
prefix="--annotations-to-exclude",
position=3,
shell_quote=False,
doc=
"Which annotations to exclude. Note: Takes presedence over arguements specified in 'annotation/annotation-groups'.\nSee https://gatk.broadinstitute.org/hc/en-us/articles/4405443524763--Tool-Documentation-Index#VariantAnnotations for valid options",
),
ToolInput(
"enableAllAnnotations",
Boolean(optional=True),
prefix="--enable-all-annotations",
position=3,
shell_quote=False,
doc=
"Use all possible annotations, will exclude those specified in --annotations-to-exclude. Note that some annotations may not be actually applied if they are not applicable to the data provided or if they are unavailable to the tool.",
),
ToolInput(
"comparisonVcf",
String(optional=True),
prefix="--comp",
position=3,
shell_quote=False,
doc=
"If a call overlaps with the provided comparison track, the INFO field with be annotated as with the track name. (i.e. --comp:FOO will have 'FOO' in the INFO field). Records that are filtered in the comparison tack will be ignored. Note that 'dbSNP' is a special case (see --dbsnp).",
),
ToolInput(
"dbSNP",
VcfTabix(optional=True),
prefix="--dbsnp",
position=3,
shell_quote=False,
doc="dbSNP reference file",
),
ToolInput(
"resource",
Vcf(optional=True),
prefix="--resource",
position=3,
shell_quote=False,
doc=
"An external resource VCF from which to pull annotations, use in combination with--expression. (i.e. to annotation with the AC field from a 'resource.vcf', specify '--resource:my_resource resource.vcf --expression my_resource.AC'. This will appear in the output as 'my_resource.AC=N').Note that if there are multiple records in the resource file that overlap the given position, one is chosen randomly. Check for allele concordance if using --resource-allele-concordance, otherwise the match is based on position only.",
),
ToolInput(
"resourceAlleleConcordance",
Boolean(optional=True),
prefix="--resource-allele-concordance",
position=3,
shell_quote=False,
doc=
"Boolean to denote if annotations (specified by --expression) from an external resource (specified by --resource) to the input VCF (specified by --variant) are to only be added if and only if the alleles are concordant between input and the resource VCFs. Otherwise always add the annotations. [Default: False]",
),
## Filter VCF
ToolInput(
"filterExpression",
String(optional=True),
prefix="--expression",
position=3,
shell_quote=False,
doc=
"one or more expressions to apply to variant calls. [Default: none]",
),
ToolInput(
"readFilter",
String(optional=True),
prefix="--read-filter",
position=3,
shell_quote=False,
doc="Read filters to be applied before analysis. [Default: none]",
),
ToolInput(
"disableReadFilter",
String(optional=True),
prefix="--disable-read-filter",
position=3,
shell_quote=False,
doc="Read filters to be disabled before analysis. [Default: none]",
),
ToolInput(
"excludeIntervals",
String(optional=True),
prefix="--exclude-intervals",
position=3,
shell_quote=False,
doc=
"Genomic intervals to exclude from analysis. This argument can be specified multiple times. You can use samtools-style intervals (i.e. 1:100-200) either explicitly on the command line or by providing a bed file. [Default: none]",
),
ToolInput(
"intervalExclusionPadding",
Int(optional=True),
prefix="--interval-exclusion-padding",
position=3,
shell_quote=False,
doc=
"Amount of padding (in bp) to add to each interval to be excluded. [Default: 0]",
),
ToolInput(
"intervalMerging",
String(optional=True),
prefix="--interval-merging-rule",
position=3,
shell_quote=False,
doc=
"Interval merging rule for abutting intervals. By default abutting (intervals that are side-by-side but not overlapping), into one continuous interval. This behaviour can be changed to treat them as separate intervals. [Default: ALL]\nValid inputs: ALL | OVERLAPPING_ONLY",
),
ToolInput(
"intervalPadding",
Int(optional=True),
prefix="--interval-padding",
position=3,
shell_quote=False,
doc=
"Amount of padding (in bp) to add to each interval you are including. [Default: 0]",
),
ToolInput(
"intervalSetRule",
String(optional=True),
prefix="--interval-set-rule",
position=3,
shell_quote=False,
doc=
"Set merging approach for combining interval inputs. When --interval are set for several intervals. The UNION of these intervals is taken. This may be changed to INTERSECTION of each specified interval, for example to only analyse the chromosome regions of an exome, this could be specified as '--interval exome.bed --interval 1 --interval-set-rule INTERSECTION'. [Default: UNION]\nValid inputs: UNION | INTERSECTION",
),
## Output options
ToolInput(
"createOutputBamIndex",
Boolean(optional=True),
prefix="--create-output-bam-index",
position=3,
shell_quote=False,
doc=
"If true, create an index, when writing a coordinate-sorted BAM/CRAM. [Default: true]",
),
ToolInput(
"createOutputVariantIndex",
Boolean(optional=True),
prefix="--create-output-variant-index",
position=3,
shell_quote=False,
doc=
"If true, create a VCF index, when writing a coordinate-sorted VCF. [Default: true]",
),
ToolInput(
"sitesOnlyVcfOutput",
Boolean(optional=True),
prefix="--sites-only-vcf-output",
position=3,
shell_quote=False,
doc=
"If true, do not output genotype fields when writing vcf outputs. [Default: false]",
),
ToolInput(
"tmpDir",
Directory(optional=True),
prefix="--tmp-dir",
position=3,
shell_quote=False,
doc="Location of a temporary directory to use",
),
ToolInput(
"verbosity",
String(optional=True),
prefix="--verbosity",
position=3,
shell_quote=False,
doc=
"Controls the verbosity of logging. [Default: INFO]\nValid input: ERROR | WARNING | INFO | DEBUG",
),
## Pedigree
ToolInput(
"pedigree",
File(optional=True),
prefix="--pedigree",
position=3,
shell_quote=False,
doc=
"Pedigree file for determining the population 'founders'. [Default: none]",
),
ToolInput(
"founderId",
String(optional=True),
prefix="--founder-id",
position=3,
shell_quote=False,
doc=
"Samples representing the population of founders. [Default: none]",
),
]