QIIME (version 2)

Note

The modules were tested on qiime version 2018.11

qiime2_import

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

A module for running qiime tools import on various importable types

Note

Tested on qiime2 version 2018.11

Requires

• If importing reads:

  • sample_data[<sample>]["fastq.F|R|S"]

• If importing other types, requires that type in the sample file

  The file can be defined in the sample file either just as a path, or as a path, format pair, as follows:

  Only path:

  EMPSingleEndSequences       /path/to/emp-single-end-sequences
  

  Path, format pair:

  EMPSingleEndSequences       /path/to/emp-single-end-sequences
  EMPSingleEndSequences       EMPPairedEndDirFmt
  

Output:

• If importing reads, will create the imported artifact in one of:

  • sample_data["project_data"]["SampleData[SequencesWithQuality]"]

  • sample_data["project_data"]["SampleData[PairedEndSequencesWithQuality]"]

• If importing other types:

  • sample_data["project_data"]["<type imported>"]

Parameters that can be set

Lines for parameter file

Importing paired end reads:

import_reads:
    module:                     qiime2_import
    base:                       trim1
    script_path:                qiime tools import
    redirects:
        --type:                 SampleData[PairedEndSequencesWithQuality]
        --input-format:         PairedEndFastqManifestPhred33

Importing internal types:

merge_data:
    module:   Import
   src:            EMPSingleEndSequences
    trg:            EMPSingleEndSequences
    script_path:    ..import..
    scope:          project

import:
    module:         qiime2_import
    base:           merge_data
    script_path:    qiime tools import

References

Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M. and Asnicar, F., 2018. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6:e27295v1 https://doi.org/10.7287/peerj.preprints.27295v1

qiime2_general

Authors

Menachem Sklarz

Affiliation

Bioinformatics core facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

Attention

This module is in Beta version. It is not issue-free and will be improved periodically.

A module to include any QIIME2 plugin method, pipeline or visualiation.

The required plugin and method are specified in the script_path line, as they would appear in the command line, e.g.:

script_path:   qiime dada2 denoise-paired

The module will identify the required inputs for the method and extract them from the appropriate slots. If they are not found, an exception will be thrown.

If more than one type is legitimate fdr a method, and both exist in the project, NeatSeq-Flow will complain. You can either remove the extra type with manage_types module or specify the type to use with the type parameter.

Plugins which require metadata files, passed as argument --m-metadata-file, will look for a file in slot metadata. In order to specify a metadata file in the parameter file, pass the --m-metadata-file in the redirects section.

All redirects argument values are searched for in the “project_data”. Thus, you can specify slots to use for redirected arguments.

Requires

Plugin- and method-specific.

Output:

Plugin- and method-specific.

Parameters that can be set

Parameter	Values	Comments
store_output	list of output parameters	These parameters will be stored as file types for use by downstream modules
export_o_params	empty or list of output parameters	If empty, all outputs will be exported, i.e. unzipped with qiime tools export. If list of parameters, only those types will be exported.

Lines for parameter file

DADA2 plugin, with export of stats output:

dada2:                      # Name of this step
    module:                     qiime2_general
    base:                       import
    script_path:                qiime dada2 denoise-single #paired
    export_o_params:
        - --o-denoising-stats
    redirects:
        --p-trim-left:         10
        --p-trunc-len:         100

Classical visualization. Only base and script_path:

dada2_vis_summary:                      # Name of this step
    module:                     qiime2_general
    base:                       dada2
    script_path:                qiime feature-table summarize

Store only particular outputs in type index:

diversity:                      # Name of this step
    module:                     qiime2_general
    base:                       phylogeny
    script_path:                qiime diversity core-metrics-phylogenetic
    export_o_params:                     --o-rarefied-table
    store_output:
        - --o-rarefied-table
        - --o-faith-pd-vector
        - --o-weighted-unifrac-distance-matrix
        - --o-weighted-unifrac-pcoa-results
        - --o-weighted-unifrac-emperor
    redirects:
        --p-sampling-depth:     50000

taxonomy_tabulate:                      # Name of this step
    module:                     qiime2_general
    base:                       taxonomy
    script_path:                qiime metadata tabulate
    redirects:
        --m-input-file:         "{{FeatureData[Taxonomy]}}"

References

Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., Abnet, C., Al-Ghalith, G.A., Alexander, H., Alm, E.J., Arumugam, M. and Asnicar, F., 2018. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints 6:e27295v1 https://doi.org/10.7287/peerj.preprints.27295v1