Formats

plugin: genome-sampler

type: directory

files:

name	path	format	required
included	included.txt	UNIXListFormat	True
excluded	excluded.txt	UNIXListFormat	True
metadata	metadata.tsv	IDMetadataFormat	True
label	label.txt	UNIXListFormat	True

type: text file

type: text file

plugin: genome-sampler

type: directory

files:

name	path	format	required
file	mask.tsv	VCFMaskFormat	True

type: text file

plugin: metadata

type: directory

files:

name	path	format	required
file	artificial-groupings.tsv	ArtificialGroupingFormat	True

plugin: types

type: directory

files:

name	path	format	required
idx1	.+(?<!\.rev)\.1\.bt2l?	Bowtie2IndexFileFormat	True
idx2	.+(?<!\.rev)\.2\.bt2l?	Bowtie2IndexFileFormat	True
ref3	.+\.3\.bt2l?	Bowtie2IndexFileFormat	True
ref4	.+\.4\.bt2l?	Bowtie2IndexFileFormat	True
rev1	.+\.rev\.1\.bt2l?	Bowtie2IndexFileFormat	True
rev2	.+\.rev\.2\.bt2l?	Bowtie2IndexFileFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	distance-matrix.tsv	LSMatFormat	True

Format for a 2+ column TSV file with an expected minimal header.

The only header recognized by this format is:

Feature ID<tab>Taxon

Optionally followed by other arbitrary columns.

This format supports blank lines. The expected header must be the first non-blank line. In addition to the header, there must be at least one line of data.

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	taxonomy.tsv	TSVTaxonomyFormat	True

Format for a 2+ column TSV file without a header.

This format supports comment lines starting with #, and blank lines.

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	taxonomy.tsv	HeaderlessTSVTaxonomyFormat	True

Legacy format for any 2+ column TSV file, with or without a header.

This format has been superseded by taxonomy file formats explicitly with and without headers, TSVTaxonomyFormat and HeaderlessTSVTaxonomyFormat, respectively.

This format remains in place for backwards-compatibility. Transformers are intentionally not hooked up to transform this format into the canonical .qza format (TSVTaxonomyFormat) to prevent users from importing data in this format. Transformers will remain in place to transform this format into in-memory Python objects (e.g. pd.Series) so that existing .qza files can still be loaded and processed.

The only header recognized by this format is:

Feature ID<tab>Taxon

Optionally followed by other arbitrary columns.

If this header isn't present, the format is assumed to be headerless.

This format supports comment lines starting with #, and blank lines.

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	taxonomy.tsv	TaxonomyFormat	True

type: text file

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	dna-sequences.fasta	DNAFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
left_dna_sequences	left-dna-sequences.fasta	DNAFASTAFormat	True
right_dna_sequences	right-dna-sequences.fasta	DNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	aligned-dna-sequences.fasta	AlignedDNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	differentials.tsv	DifferentialFormat	True

type: text file

type: text file

type: text file

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	protein-sequences.fasta	ProteinFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
file	aligned-protein-sequences.fasta	AlignedProteinFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
file	protein-sequences.fasta	MixedCaseProteinFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
file	aligned-protein-sequences.fasta	MixedCaseAlignedProteinFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	rna-sequences.fasta	RNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	aligned-rna-sequences.fasta	AlignedRNAFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
left_rna_sequences	left-rna-sequences.fasta	RNAFASTAFormat	True
right_rna_sequences	right-rna-sequences.fasta	RNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	blast6.tsv	BLAST6Format	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	dna-sequences.fasta	MixedCaseDNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	rna-sequences.fasta	MixedCaseRNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	aligned-dna-sequences.fasta	MixedCaseAlignedDNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	aligned-rna-sequences.fasta	MixedCaseAlignedRNAFASTAFormat	True

Format for a TSV file with information about sequences like length of a feature. The first column contains feature identifiers and is followed by other optional columns.

The file cannot be empty and must have at least two columns.

Validation for additional columns can be added with a semantic validator tied to a property. For example the "validate_seq_char_len" validator for "FeatureData[SequenceCharacteristics % Properties("length")]" adds validation for a numerical column called "length".

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	sequence_characteristics.tsv	SequenceCharacteristicsFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$	DNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	mag-to-contigs.json	MAGtoContigsFormat	True

type: text file

type: binary file

plugin: types

type: directory

files:

name	path	format	required
file	feature-table.biom	BIOMV100Format	True

plugin: types

type: directory

files:

name	path	format	required
file	feature-table.biom	BIOMV210Format	True

plugin: types

type: directory

files:

name	path	format	required
genes	.+\.(fa|fna|fasta)$	DNAFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
proteins	.+\.(fa|faa|fasta)$	ProteinFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
loci	.+\.gff$	GFF3Format	True

plugin: types

type: directory

files:

name	path	format	required
genomes	.+\.(fasta|fa)$	DNAFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
seed_orthologs	.*\..*\.seed_orthologs	OrthologFileFmt	True

plugin: types

type: directory

files:

name	path	format	required
annotations	.+\.annotations	OrthologFileFmt	True

Generic Feature Format Version 3 (GFF3) spec: gff3.md NCBI modifications to the above: https://www.ncbi.nlm.nih.gov/datasets/docs/reference-docs/file-formats/about-ncbi-gff3/

type: text file

plugin: types

type: directory

files:

name	path	format	required
nodes	nodes.dmp	NCBITaxonomyNodesFormat	True
names	names.dmp	NCBITaxonomyNamesFormat	True
index	kaiju_db.+\.fmi	KaijuIndexFormat	True

type: binary file

type: text file

type: text file

type: text file

type: text file

plugin: types

type: directory

files:

name	path	format	required
reports	.+report\.(txt|tsv)$	Kraken2ReportFormat	True

plugin: types

type: directory

files:

name	path	format	required
reports	.+output\.(txt|tsv)$	Kraken2OutputFormat	True

plugin: types

type: directory

files:

name	path	format	required
hash	hash.k2d	Kraken2DBFormat	True
opts	opts.k2d	Kraken2DBFormat	True
taxo	taxo.k2d	Kraken2DBFormat	True

plugin: types

type: directory

files:

name	path	format	required
file	report.txt	Kraken2DBReportFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
kmers	database(\d{2,})mers\.kmer_distrib$	BrackenDBFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	metadata.tsv	ImmutableMetadataFormat	True

plugin: types

type: directory

files:

name	path	format	required
file	forward.fastq.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
forward_sequences	forward.fastq.gz	FastqGzFormat	True
reverse_sequences	reverse.fastq.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	reads.fasta	DNAFASTAFormat	True
quality	reads.qual	QualFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	sequences.fastq.gz	FastqGzFormat	True
barcodes	barcodes.fastq.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
file	details.tsv	ErrorCorrectionDetailsFmt	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
sequences	sequences.fastq.gz	FastqGzFormat	True
barcodes	barcodes.fastq.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	Undetermined_S0_L001_R1_001.fastq.gz	FastqGzFormat	True
barcodes	Undetermined_S0_L001_I1_001.fastq.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
forward	forward.fastq.gz	FastqGzFormat	True
reverse	reverse.fastq.gz	FastqGzFormat	True
barcodes	barcodes.fastq.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
forward	Undetermined_S0_L001_R1_001.fastq.gz	FastqGzFormat	True
reverse	Undetermined_S0_L001_R2_001.fastq.gz	FastqGzFormat	True
barcodes	Undetermined_S0_L001_I1_001.fastq.gz	FastqGzFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	ordination.txt	OrdinationFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	ProcrustesStatistics.tsv	ProcrustesStatisticsFmt	True

Mapping of sample identifiers to relative filepaths and read direction.

type: text file

Mapping of sample identifiers to absolute filepaths and read direction.

type: text file

Arbitrary yaml-formatted file.

type: text file

A gzipped fastq file.

type: binary file

plugin: types

type: directory

files:

name	path	format	required
sequences	.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	.+_.+_R[12]_001\.fastq\.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz	FastqGzFormat	True
manifest	MANIFEST	FastqManifestFormat	True
metadata	metadata.yml	YamlFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz	FastqGzFormat	True
manifest	MANIFEST	FastqManifestFormat	True
metadata	metadata.yml	YamlFormat	True

type: text file

type: text file

type: text file

type: text file

type: text file

type: text file

type: text file

type: text file

QIIME 1 demultiplexed FASTA format.

The QIIME 1 demultiplexed FASTA format is the default output format of split_libraries.py and split_libraries_fastq.py. The file output by QIIME 1 is named seqs.fna; this filename is sometimes associated with the file format itself due to its widespread usage in QIIME 1.

The format is documented here: http://qiime.org/documentation/file_formats.html#demultiplexed-sequences

Format details:

- FASTA file with exactly two lines per record: header and sequence. Each sequence must span exactly one line and cannot be split across multiple lines.

- The ID in each header must follow the format <sample-id>_<seq-id>. <sample-id> is the identifier of the sample the sequence belongs to, and <seq-id> is an identifier for the sequence within its sample. In QIIME 1, <seq-id> is typically an incrementing integer starting from zero, but any non-empty value can be used here, as long as the header IDs remain unique throughout the file. Note: <sample-id> may contain sample IDs that contain underscores; the rightmost underscore will used to delimit sample and sequence IDs.

- Descriptions in headers are permitted and ignored.

- Header IDs must be unique within the file.

- Each sequence must be DNA and cannot be empty.

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	seqs.fna	QIIME1DemuxFormat	True

Single-end reads in fastq.gz files where base filename is the sample id

The full file name, minus the extension (.fastq.gz) is the sample id. For example, the sample id for the file: * sample-1.fastq.gz is sample-1 * xyz.fastq.gz is xyz * sample-42_S1_L001_R1_001.fastq.gz is sample-42_S1_L001_R1_001

plugin: types

type: directory

files:

name	path	format	required
sequences	.+\.fastq\.gz	FastqGzFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	.+\.(fa|fasta)$	DNAFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	.+\.(fa|fasta)$	DNAFASTAFormat	True
manifest	MANIFEST	MultiMAGManifestFormat	True

plugin: types

type: directory

files:

name	path	format	required
sequences	[^\.].+_contigs.(fasta|fa)$	DNAFASTAFormat	True

plugin: types

type: directory

files:

name	path	format	required
idx1	.+(?<!\.rev)\.1\.bt2l?	Bowtie2IndexFileFormat	True
idx2	.+(?<!\.rev)\.2\.bt2l?	Bowtie2IndexFileFormat	True
ref3	.+\.3\.bt2l?	Bowtie2IndexFileFormat	True
ref4	.+\.4\.bt2l?	Bowtie2IndexFileFormat	True
rev1	.+\.rev\.1\.bt2l?	Bowtie2IndexFileFormat	True
rev2	.+\.rev\.2\.bt2l?	Bowtie2IndexFileFormat	True

type: binary file

plugin: types

type: directory

files:

name	path	format	required
bams	.+\.bam	BAMFormat	True

plugin: types

type: directory

files:

name	path	format	required
bams	.+\/.+\.bam	BAMFormat	True

type: text file

type: text file

type: text file

type: text file

type: text file

type: text file

type: text file

The <hmmfile>.h3m file contains the profile HMMs and their annotation in a binary format. The <hmmfile>.h3i file is an SSI index for the <hmmfile>.h3m file. The <hmmfile>.h3f file contains precomputed data structures for the fast heuristic filter (the MSV filter). The <hmmfile>.h3p file contains precomputed data structures for the rest of each profile.

plugin: types

type: directory

files:

name	path	format	required
h3m	.*\.hmm\.h3m	ProfileHmmBinaryFileFmt	True
h3i	.*\.hmm\.h3i	ProfileHmmBinaryFileFmt	True
h3f	.*\.hmm\.h3f	ProfileHmmBinaryFileFmt	True
h3p	.*\.hmm\.h3p	ProfileHmmBinaryFileFmt	True

plugin: types

type: directory

files:

name	path	format	required
profile	.*\.hmm	ProteinSingleProfileHmmFileFmt	True

plugin: types

type: directory

files:

name	path	format	required
profiles	.*\.hmm	ProteinMultipleProfileHmmFileFmt	True

plugin: types

type: directory

files:

name	path	format	required
profile	.*\.hmm	DNASingleProfileHmmFileFmt	True

plugin: types

type: directory

files:

name	path	format	required
profiles	.*\.hmm	DNAMultipleProfileHmmFileFmt	True

plugin: types

type: directory

files:

name	path	format	required
profile	.*\.hmm	RNASingleProfileHmmFileFmt	True

plugin: types

type: directory

files:

name	path	format	required
profiles	.*\.hmm	RNAMultipleProfileHmmFileFmt	True

type: text file

type: binary file

plugin: types

type: directory

files:

name	path	format	required
eggnog	eggnog.*db.*	EggnogRefBinFileFmt	True

type: binary file

plugin: types

type: directory

files:

name	path	format	required
file	ref_db.dmnd	DiamondDatabaseFileFmt	True

type: text file

type: text file

type: binary file

plugin: types

type: directory

files:

name	path	format	required
node	nodes.dmp	NCBITaxonomyNodesFormat	True
names	names.dmp	NCBITaxonomyNamesFormat	True
tax_map	prot.accession2taxid.gz	NCBITaxonomyBinaryFileFmt	True

plugin: types

type: directory

files:

name	path	format	required
taxid_info	e5.taxid_info.tsv	EggnogRefTextFileFmt	True
proteins	e5.proteomes.faa	MixedCaseProteinFASTAFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	alpha-diversity.tsv	AlphaDiversityFormat	True

type: text file

plugin: types

type: directory

files:

name	path	format	required
file	tree.nwk	NewickFormat	True