Formats
assembly¶
QUASTResultsFormat¶
- type: text file
QUASTResultsDirectoryFormat¶
- plugin: assembly
- type: directory
- files:
name path format required file quast_results.tsvQUASTResultsFormatTrue
metadata¶
ArtificialGroupingFormat¶
- type: text file
ArtificialGroupingDirectoryFormat¶
- plugin: metadata
- type: directory
- files:
name path format required file artificial-groupings.tsvArtificialGroupingFormatTrue
annotate¶
BUSCOResultsFormat¶
- type: text file
BUSCOResultsDirectoryFormat¶
- plugin: annotate
- type: directory
- files:
name path format required file busco_results.tsvBUSCOResultsFormatTrue
BuscoDatabaseDirFmt¶
- plugin: annotate
- type: directory
- files:
name path format required ancestral lineages\/.+\/ancestral$BuscoGenericTextFileFmtFalse ancestral_variants lineages\/.+\/ancestral_variants$BuscoGenericTextFileFmtFalse dataset lineages\/.+\/dataset\.cfg$BuscoGenericTextFileFmtFalse hmms lineages\/.+\/hmms\/.+\.hmm$BuscoGenericTextFileFmtFalse lengths_cutoff lineages\/.+\/lengths_cutoff$BuscoGenericTextFileFmtFalse links_to_ODB lineages\/.+\/links_to_ODB.+\.txt$BuscoGenericTextFileFmtFalse ogs_id lineages\/.+\/info\/ogs\.id\.info$BuscoGenericTextFileFmtFalse refseq_db_md5 lineages\/.+\/refseq_db\.faa\.gz\.md5BuscoGenericTextFileFmtFalse scores_cutoff lineages\/.+\/scores_cutoff$BuscoGenericTextFileFmtFalse species lineages\/.+\/info\/species\.info$BuscoGenericTextFileFmtFalse list_of_reference_markers placement_files\/list_of_reference_markers\..+\.txt$BuscoGenericTextFileFmtFalse mapping_taxid_lineage placement_files\/mapping_taxid-lineage\..+\.txt$BuscoGenericTextFileFmtFalse mapping_taxids_busco_dataset_name placement_files\/mapping_taxids-busco_dataset_name\..+\.txt$BuscoGenericTextFileFmtFalse tree placement_files\/tree\..+\.nwk$BuscoGenericTextFileFmtFalse tree_metadata placement_files\/tree_metadata\..+\.txt$BuscoGenericTextFileFmtFalse supermatrix_aln placement_files\/supermatrix\.aln\..+\.faa$AlignedProteinFASTAFormatFalse prfls lineages\/.+\/prfl\/.+\.prfl$BuscoGenericTextFileFmtFalse version_file file_versions.tsvBuscoGenericTextFileFmtTrue refseq_db lineages\/.+refseq_db\.faa(\.gz)?BuscoGenericBinaryFileFmtFalse information information\/.+\.txt$BuscoGenericTextFileFmtFalse missing_parasitic lineages\/.+\/missing_in_parasitic\.txt$BuscoGenericTextFileFmtFalse no_hits lineages\/.+\/no_hits$BuscoGenericTextFileFmtFalse
EggnogHmmerIdmapFileFmt¶
- type: text file
EggnogHmmerIdmapDirectoryFmt¶
- plugin: annotate
- type: directory
- files:
name path format required idmap .*\.hmm\.idmapEggnogHmmerIdmapFileFmtTrue
sourmash¶
MinHashSigJson¶
- type: text file
MinHashSigJsonDirFormat¶
- plugin: sourmash
- type: directory
- files:
name path format required signatures .*\.sigMinHashSigJsonTrue
rescript¶
SILVATaxonomyFormat¶
- type: text file
SILVATaxonomyDirectoryFormat¶
- plugin: rescript
- type: directory
- files:
name path format required file silva_taxonomy.tsvSILVATaxonomyFormatTrue
SILVATaxidMapFormat¶
- type: text file
SILVATaxidMapDirectoryFormat¶
- plugin: rescript
- type: directory
- files:
name path format required file silva_taxmap.tsvSILVATaxidMapFormatTrue
quality-filter¶
QualityFilterStatsFmt¶
- type: text file
QualityFilterStatsDirFmt¶
- plugin: quality-filter
- type: directory
- files:
name path format required file stats.csvQualityFilterStatsFmtTrue
longitudinal¶
FirstDifferencesFormat¶
- type: text file
FirstDifferencesDirectoryFormat¶
- plugin: longitudinal
- type: directory
- files:
name path format required file FirstDifferences.tsvFirstDifferencesFormatTrue
types¶
Bowtie2IndexDirFmt¶
- plugin: types
- type: directory
- files:
name path format required idx1 .+(?<!\.rev)\.1\.bt2l?Bowtie2IndexFileFormatTrue idx2 .+(?<!\.rev)\.2\.bt2l?Bowtie2IndexFileFormatTrue ref3 .+\.3\.bt2l?Bowtie2IndexFileFormatTrue ref4 .+\.4\.bt2l?Bowtie2IndexFileFormatTrue rev1 .+\.rev\.1\.bt2l?Bowtie2IndexFileFormatTrue rev2 .+\.rev\.2\.bt2l?Bowtie2IndexFileFormatTrue
LSMatFormat¶
- type: text file
DistanceMatrixDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file distance-matrix.tsvLSMatFormatTrue
TSVTaxonomyFormat¶
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
TSVTaxonomyDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file taxonomy.tsvTSVTaxonomyFormatTrue
HeaderlessTSVTaxonomyFormat¶
Format for a 2+ column TSV file without a header.
This format supports comment lines starting with #, and blank lines.
- type: text file
HeaderlessTSVTaxonomyDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file taxonomy.tsvHeaderlessTSVTaxonomyFormatTrue
TaxonomyFormat¶
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
TaxonomyDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file taxonomy.tsvTaxonomyFormatTrue
FASTAFormat¶
- type: text file
DNAFASTAFormat¶
- type: text file
DNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file dna-sequences.fastaDNAFASTAFormatTrue
PairedDNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required left_dna_sequences left-dna-sequences.fastaDNAFASTAFormatTrue right_dna_sequences right-dna-sequences.fastaDNAFASTAFormatTrue
AlignedDNAFASTAFormat¶
- type: text file
AlignedDNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file aligned-dna-sequences.fastaAlignedDNAFASTAFormatTrue
DifferentialFormat¶
- type: text file
DifferentialDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file differentials.tsvDifferentialFormatTrue
ProteinFASTAFormat¶
- type: text file
AlignedProteinFASTAFormat¶
- type: text file
MixedCaseProteinFASTAFormat¶
- type: text file
MixedCaseAlignedProteinFASTAFormat¶
- type: text file
ProteinSequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file protein-sequences.fastaProteinFASTAFormatTrue
AlignedProteinSequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file aligned-protein-sequences.fastaAlignedProteinFASTAFormatTrue
MixedCaseProteinSequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file protein-sequences.fastaMixedCaseProteinFASTAFormatTrue
MixedCaseAlignedProteinSequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file aligned-protein-sequences.fastaMixedCaseAlignedProteinFASTAFormatTrue
RNAFASTAFormat¶
- type: text file
RNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file rna-sequences.fastaRNAFASTAFormatTrue
AlignedRNAFASTAFormat¶
- type: text file
AlignedRNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file aligned-rna-sequences.fastaAlignedRNAFASTAFormatTrue
PairedRNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required left_rna_sequences left-rna-sequences.fastaRNAFASTAFormatTrue right_rna_sequences right-rna-sequences.fastaRNAFASTAFormatTrue
BLAST6Format¶
- type: text file
BLAST6DirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file blast6.tsvBLAST6FormatTrue
MixedCaseDNAFASTAFormat¶
- type: text file
MixedCaseDNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file dna-sequences.fastaMixedCaseDNAFASTAFormatTrue
MixedCaseRNAFASTAFormat¶
- type: text file
MixedCaseRNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file rna-sequences.fastaMixedCaseRNAFASTAFormatTrue
MixedCaseAlignedDNAFASTAFormat¶
- type: text file
MixedCaseAlignedDNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file aligned-dna-sequences.fastaMixedCaseAlignedDNAFASTAFormatTrue
MixedCaseAlignedRNAFASTAFormat¶
- type: text file
MixedCaseAlignedRNASequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file aligned-rna-sequences.fastaMixedCaseAlignedRNAFASTAFormatTrue
SequenceCharacteristicsFormat¶
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
SequenceCharacteristicsDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file sequence_characteristics.tsvSequenceCharacteristicsFormatTrue
MAGSequencesDirFmt¶
- 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)$DNAFASTAFormatTrue
MAGtoContigsFormat¶
- type: text file
MAGtoContigsDirFmt¶
- plugin: types
- type: directory
- files:
name path format required file mag-to-contigs.jsonMAGtoContigsFormatTrue
BIOMV100Format¶
- type: text file
BIOMV210Format¶
- type: binary file
BIOMV100DirFmt¶
- plugin: types
- type: directory
- files:
name path format required file feature-table.biomBIOMV100FormatTrue
BIOMV210DirFmt¶
- plugin: types
- type: directory
- files:
name path format required file feature-table.biomBIOMV210FormatTrue
GenesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required genes .+\.(fa|fna|fasta)$DNAFASTAFormatTrue
ProteinsDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required proteins .+\.(fa|faa|fasta)$ProteinFASTAFormatTrue
LociDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required loci .+\.gff$GFF3FormatTrue
GenomeSequencesDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required genomes .+\.(fasta|fa)$DNAFASTAFormatTrue
OrthologFileFmt¶
- type: text file
SeedOrthologDirFmt¶
- plugin: types
- type: directory
- files:
name path format required seed_orthologs .*\..*\.seed_orthologsOrthologFileFmtTrue
OrthologAnnotationDirFmt¶
- plugin: types
- type: directory
- files:
name path format required annotations .+\.annotationsOrthologFileFmtTrue
GFF3Format¶
Generic Feature Format Version 3 (GFF3) spec:
gff3.md
NCBI modifications to the above:
https://
- type: text file
KaijuDBDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required nodes nodes.dmpNCBITaxonomyNodesFormatTrue names names.dmpNCBITaxonomyNamesFormatTrue index kaiju_db.+\.fmiKaijuIndexFormatTrue
KaijuIndexFormat¶
- type: binary file
Kraken2ReportFormat¶
- type: text file
Kraken2OutputFormat¶
- type: text file
Kraken2DBFormat¶
- type: text file
Kraken2DBReportFormat¶
- type: text file
Kraken2ReportDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required reports .+\.report\.(txt|tsv)$Kraken2ReportFormatTrue
Kraken2OutputDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required outputs .+\.output\.(txt|tsv)$Kraken2OutputFormatTrue
Kraken2DBDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required hash hash.k2dKraken2DBFormatTrue opts opts.k2dKraken2DBFormatTrue taxo taxo.k2dKraken2DBFormatTrue
Kraken2DBReportDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file report.txtKraken2DBReportFormatTrue
BrackenDBFormat¶
- type: text file
BrackenDBDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required kmers database(\d{2,})mers\.kmer_distrib$BrackenDBFormatTrue
ImmutableMetadataFormat¶
- type: text file
ImmutableMetadataDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file metadata.tsvImmutableMetadataFormatTrue
MultiplexedSingleEndBarcodeInSequenceDirFmt¶
- plugin: types
- type: directory
- files:
name path format required file forward.fastq.gzFastqGzFormatTrue
MultiplexedPairedEndBarcodeInSequenceDirFmt¶
- plugin: types
- type: directory
- files:
name path format required forward_sequences forward.fastq.gzFastqGzFormatTrue reverse_sequences reverse.fastq.gzFastqGzFormatTrue
MultiplexedFastaQualDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences reads.fastaDNAFASTAFormatTrue quality reads.qualQualFormatTrue
EMPMultiplexedDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences sequences.fastq.gzFastqGzFormatTrue barcodes barcodes.fastq.gzFastqGzFormatTrue
ErrorCorrectionDetailsDirFmt¶
- plugin: types
- type: directory
- files:
name path format required file details.tsvErrorCorrectionDetailsFmtTrue
ErrorCorrectionDetailsFmt¶
- type: text file
EMPSingleEndDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences sequences.fastq.gzFastqGzFormatTrue barcodes barcodes.fastq.gzFastqGzFormatTrue
EMPSingleEndCasavaDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences Undetermined_S0_L001_R1_001.fastq.gzFastqGzFormatTrue barcodes Undetermined_S0_L001_I1_001.fastq.gzFastqGzFormatTrue
EMPPairedEndDirFmt¶
- plugin: types
- type: directory
- files:
name path format required forward forward.fastq.gzFastqGzFormatTrue reverse reverse.fastq.gzFastqGzFormatTrue barcodes barcodes.fastq.gzFastqGzFormatTrue
EMPPairedEndCasavaDirFmt¶
- plugin: types
- type: directory
- files:
name path format required forward Undetermined_S0_L001_R1_001.fastq.gzFastqGzFormatTrue reverse Undetermined_S0_L001_R2_001.fastq.gzFastqGzFormatTrue barcodes Undetermined_S0_L001_I1_001.fastq.gzFastqGzFormatTrue
OrdinationFormat¶
- type: text file
OrdinationDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file ordination.txtOrdinationFormatTrue
ProcrustesStatisticsFmt¶
- type: text file
ProcrustesStatisticsDirFmt¶
- plugin: types
- type: directory
- files:
name path format required file ProcrustesStatistics.tsvProcrustesStatisticsFmtTrue
FastqManifestFormat¶
Mapping of sample identifiers to relative filepaths and read direction.
- type: text file
FastqAbsolutePathManifestFormat¶
Mapping of sample identifiers to absolute filepaths and read direction.
- type: text file
YamlFormat¶
Arbitrary yaml-formatted file.
- type: text file
FastqGzFormat¶
A gzipped fastq file.
- type: binary file
CasavaOneEightSingleLanePerSampleDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gzFastqGzFormatTrue
CasavaOneEightLanelessPerSampleDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences .+_.+_R[12]_001\.fastq\.gzFastqGzFormatTrue
SingleLanePerSampleSingleEndFastqDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gzFastqGzFormatTrue manifest MANIFESTFastqManifestFormatTrue metadata metadata.ymlYamlFormatTrue
SingleLanePerSamplePairedEndFastqDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences .+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gzFastqGzFormatTrue manifest MANIFESTFastqManifestFormatTrue metadata metadata.ymlYamlFormatTrue
SingleEndFastqManifestPhred33¶
- type: text file
SingleEndFastqManifestPhred64¶
- type: text file
PairedEndFastqManifestPhred33¶
- type: text file
PairedEndFastqManifestPhred64¶
- type: text file
SingleEndFastqManifestPhred33V2¶
- type: text file
SingleEndFastqManifestPhred64V2¶
- type: text file
PairedEndFastqManifestPhred33V2¶
- type: text file
PairedEndFastqManifestPhred64V2¶
- type: text file
QIIME1DemuxFormat¶
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://
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
QIIME1DemuxDirFmt¶
- plugin: types
- type: directory
- files:
name path format required file seqs.fnaQIIME1DemuxFormatTrue
SampleIdIndexedSingleEndPerSampleDirFmt¶
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\.gzFastqGzFormatTrue
MultiFASTADirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required sequences .+\.(fa|fasta)$DNAFASTAFormatTrue
MultiMAGSequencesDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences .+\.(fa|fasta)$DNAFASTAFormatTrue manifest MANIFESTMultiMAGManifestFormatTrue
ContigSequencesDirFmt¶
- plugin: types
- type: directory
- files:
name path format required sequences [^\.].+_contigs.(fasta|fa)$DNAFASTAFormatTrue
MultiBowtie2IndexDirFmt¶
- plugin: types
- type: directory
- files:
name path format required idx1 .+(?<!\.rev)\.1\.bt2l?Bowtie2IndexFileFormatTrue idx2 .+(?<!\.rev)\.2\.bt2l?Bowtie2IndexFileFormatTrue ref3 .+\.3\.bt2l?Bowtie2IndexFileFormatTrue ref4 .+\.4\.bt2l?Bowtie2IndexFileFormatTrue rev1 .+\.rev\.1\.bt2l?Bowtie2IndexFileFormatTrue rev2 .+\.rev\.2\.bt2l?Bowtie2IndexFileFormatTrue
BAMFormat¶
- type: binary file
BAMDirFmt¶
MultiBAMDirFmt¶
MultiMAGManifestFormat¶
- type: text file
ProteinMultipleProfileHmmFileFmt¶
- type: text file
ProteinSingleProfileHmmFileFmt¶
- type: text file
RNAMultipleProfileHmmFileFmt¶
- type: text file
RNASingleProfileHmmFileFmt¶
- type: text file
DNAMultipleProfileHmmFileFmt¶
- type: text file
DNASingleProfileHmmFileFmt¶
- type: text file
PressedProfileHmmsDirectoryFmt¶
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\.h3mProfileHmmBinaryFileFmtTrue h3i .*\.hmm\.h3iProfileHmmBinaryFileFmtTrue h3f .*\.hmm\.h3fProfileHmmBinaryFileFmtTrue h3p .*\.hmm\.h3pProfileHmmBinaryFileFmtTrue
ProteinSingleProfileHmmDirectoryFmt¶
- plugin: types
- type: directory
- files:
name path format required profile .*\.hmmProteinSingleProfileHmmFileFmtTrue
ProteinMultipleProfileHmmDirectoryFmt¶
- plugin: types
- type: directory
- files:
name path format required profiles .*\.hmmProteinMultipleProfileHmmFileFmtTrue
DNASingleProfileHmmDirectoryFmt¶
- plugin: types
- type: directory
- files:
name path format required profile .*\.hmmDNASingleProfileHmmFileFmtTrue
DNAMultipleProfileHmmDirectoryFmt¶
- plugin: types
- type: directory
- files:
name path format required profiles .*\.hmmDNAMultipleProfileHmmFileFmtTrue
RNASingleProfileHmmDirectoryFmt¶
- plugin: types
- type: directory
- files:
name path format required profile .*\.hmmRNASingleProfileHmmFileFmtTrue
RNAMultipleProfileHmmDirectoryFmt¶
- plugin: types
- type: directory
- files:
name path format required profiles .*\.hmmRNAMultipleProfileHmmFileFmtTrue
EggnogRefTextFileFmt¶
- type: text file
EggnogRefBinFileFmt¶
- type: binary file
EggnogRefDirFmt¶
- plugin: types
- type: directory
- files:
name path format required eggnog eggnog.*db.*EggnogRefBinFileFmtTrue
DiamondDatabaseFileFmt¶
- type: binary file
DiamondDatabaseDirFmt¶
- plugin: types
- type: directory
- files:
name path format required file ref_db.dmndDiamondDatabaseFileFmtTrue
NCBITaxonomyNodesFormat¶
- type: text file
NCBITaxonomyNamesFormat¶
- type: text file
NCBITaxonomyBinaryFileFmt¶
- type: binary file
NCBITaxonomyDirFmt¶
- plugin: types
- type: directory
- files:
name path format required node nodes.dmpNCBITaxonomyNodesFormatTrue names names.dmpNCBITaxonomyNamesFormatTrue tax_map prot.accession2taxid.gzNCBITaxonomyBinaryFileFmtTrue
EggnogProteinSequencesDirFmt¶
- plugin: types
- type: directory
- files:
name path format required taxid_info e5.taxid_info.tsvEggnogRefTextFileFmtTrue proteins e5.proteomes.faaMixedCaseProteinFASTAFormatTrue
AlphaDiversityFormat¶
- type: text file
AlphaDiversityDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file alpha-diversity.tsvAlphaDiversityFormatTrue
NewickFormat¶
- type: text file
NewickDirectoryFormat¶
- plugin: types
- type: directory
- files:
name path format required file tree.nwkNewickFormatTrue
NDJSONFileFormat¶
Format for newline-delimited (ND) JSON file.
- type: text file
DataResourceSchemaFileFormat¶
Format for data resource schema.
- type: text file
TabularDataResourceDirFmt¶
- plugin: types
- type: directory
- files:
name path format required data data.ndjsonNDJSONFileFormatTrue metadata dataresource.jsonDataResourceSchemaFileFormatTrue
TableJSONLFileFormat¶
- type: text file
TableJSONLDirFmt¶
- plugin: types
- type: directory
- files:
name path format required file data.table.jsonlTableJSONLFileFormatTrue
fondue¶
SRAMetadataFormat¶
- type: text file
SRAMetadataDirFmt¶
- plugin: fondue
- type: directory
- files:
name path format required file sra-metadata.tsvSRAMetadataFormatTrue
SRAFailedIDsFormat¶
This is a "fake" format only used to store a list of failed SRA IDs, which can be converted to QIIME's metadata and input into any fondue action.
- type: text file
SRAFailedIDsDirFmt¶
- plugin: fondue
- type: directory
- files:
name path format required file sra-failed-ids.tsvSRAFailedIDsFormatTrue
NCBIAccessionIDsFormat¶
This is a format used to store a list of SRA accession IDs (run, study, BioProject, sample and experiment IDs), which can be converted to QIIME's metadata. Artifacts containing of run, study and BioProject IDs can be input into any fondue action.
- type: text file
NCBIAccessionIDsDirFmt¶
- plugin: fondue
- type: directory
- files:
name path format required file ncbi-accession-ids.tsvNCBIAccessionIDsFormatTrue
quality-control¶
DecontamScoreFormat¶
- type: text file
DecontamScoreDirFmt¶
- plugin: quality-control
- type: directory
- files:
name path format required file stats.tsvDecontamScoreFormatTrue
feature-classifier¶
BLASTDBDirFmtV5¶
- plugin: feature-classifier
- type: directory
- files:
name path format required idx1 .+\.ndbBLASTDBFileFmtV5True idx2 .+\.nhrBLASTDBFileFmtV5True idx3 .+\.ninBLASTDBFileFmtV5True idx4 .+\.notBLASTDBFileFmtV5True idx5 .+\.nsqBLASTDBFileFmtV5True idx6 .+\.ntfBLASTDBFileFmtV5True idx7 .+\.ntoBLASTDBFileFmtV5True idx8 .+\.njsBLASTDBFileFmtV5True
TaxonomicClassifierDirFmt¶
- plugin: feature-classifier
- type: directory
- files:
name path format required preprocess_params preprocess_params.jsonJSONFormatTrue sklearn_pipeline sklearn_pipeline.tarPickleFormatTrue
TaxonomicClassiferTemporaryPickleDirFmt¶
- plugin: feature-classifier
- type: directory
- files:
name path format required version_info sklearn_version.jsonJSONFormatTrue sklearn_pipeline sklearn_pipeline.tarPickleFormatTrue
sapienns¶
MetaphlanMergedAbundanceFormat¶
- type: text file
MetaphlanMergedAbundanceDirectoryFormat¶
- plugin: sapienns
- type: directory
- files:
name path format required file table.tsvMetaphlanMergedAbundanceFormatTrue
HumannPathAbundanceFormat¶
- type: text file
HumannPathAbundanceDirectoryFormat¶
- plugin: sapienns
- type: directory
- files:
name path format required file table.tsvHumannPathAbundanceFormatTrue
HumannGeneFamilyFormat¶
- type: text file
HumannGeneFamilyDirectoryFormat¶
- plugin: sapienns
- type: directory
- files:
name path format required file table.tsvHumannGeneFamilyFormatTrue
composition¶
FrictionlessCSVFileFormat¶
Format for frictionless CSV.
- type: text file
DataPackageSchemaFileFormat¶
Format for the associated metadata for each file in the DataLoaf.
- type: text file
DataLoafPackageDirFmt¶
- plugin: composition
- type: directory
- files:
name path format required data_slices .+\.csvFrictionlessCSVFileFormatTrue nutrition_facts datapackage.jsonDataPackageSchemaFileFormatTrue
ANCOMBC2OutputDirFmt¶
Stores the model statistics and optionally the structural zeros table= output by the ANCOMBC2 method.
The slices are: - lfc: log-fold change - se: standard error - W: lfc / se (the test statistic) - p: p-value - q: adjusted p-value - diff: differentially abundant boolean (i.e. q < alpha) - passed_ss: whether sensitivity analysis was passed
- plugin: composition
- type: directory
- files:
name path format required lfc lfc.jsonlTableJSONLFileFormatTrue se se.jsonlTableJSONLFileFormatTrue W W.jsonlTableJSONLFileFormatTrue p p.jsonlTableJSONLFileFormatTrue q q.jsonlTableJSONLFileFormatTrue diff diff.jsonlTableJSONLFileFormatTrue passed_ss passed_ss.jsonlTableJSONLFileFormatTrue structural_zeros structural-zeros.jsonlTableJSONLFileFormatFalse
sample-classifier¶
SampleEstimatorDirFmt¶
- plugin: sample-classifier
- type: directory
- files:
name path format required version_info sklearn_version.jsonJSONFormatTrue sklearn_pipeline sklearn_pipeline.tarPickleFormatTrue
BooleanSeriesFormat¶
- type: text file
BooleanSeriesDirectoryFormat¶
- plugin: sample-classifier
- type: directory
- files:
name path format required file outliers.tsvBooleanSeriesFormatTrue
ImportanceFormat¶
- type: text file
ImportanceDirectoryFormat¶
- plugin: sample-classifier
- type: directory
- files:
name path format required file importance.tsvImportanceFormatTrue
PredictionsFormat¶
- type: text file
PredictionsDirectoryFormat¶
- plugin: sample-classifier
- type: directory
- files:
name path format required file predictions.tsvPredictionsFormatTrue
ProbabilitiesFormat¶
- type: text file
ProbabilitiesDirectoryFormat¶
- plugin: sample-classifier
- type: directory
- files:
name path format required file class_probabilities.tsvProbabilitiesFormatTrue
TrueTargetsDirectoryFormat¶
- plugin: sample-classifier
- type: directory
- files:
name path format required file true_targets.tsvPredictionsFormatTrue
vsearch¶
UchimeStatsFmt¶
- type: text file
UchimeStatsDirFmt¶
- plugin: vsearch
- type: directory
- files:
name path format required file stats.tsvUchimeStatsFmtTrue