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qiime2-step1-import-demux-paired.cwl
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qiime2-step1-import-demux-paired.cwl
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{
"cwlVersion": "v1.0",
"$graph": [
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"label": "qiime2 importing data",
"doc": "Obtaining and importing data from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/",
"inputs": [
{
"type": "File",
"id": "#qiime2-01-import-data-paired.cwl/barcodes"
},
{
"type": "File",
"id": "#qiime2-01-import-data-paired.cwl/forward_sequences"
},
{
"type": "File",
"id": "#qiime2-01-import-data-paired.cwl/reverse_sequences"
},
{
"type": "string",
"default": "emp-paired-end-sequences.qza",
"id": "#qiime2-01-import-data-paired.cwl/sequences_artifact_filename"
},
{
"type": "string",
"default": "EMPPairedEndSequences",
"id": "#qiime2-01-import-data-paired.cwl/sequences_artifact_type"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#qiime2-01-import-data-paired.cwl/make_sequences_artifact/sequences_artifact",
"id": "#qiime2-01-import-data-paired.cwl/sequences_artifact"
}
],
"steps": [
{
"run": "#EMPPairedEndSequences-directory.cwl",
"in": [
{
"source": "#qiime2-01-import-data-paired.cwl/barcodes",
"id": "#qiime2-01-import-data-paired.cwl/make_import_directory/barcodes"
},
{
"source": "#qiime2-01-import-data-paired.cwl/forward_sequences",
"id": "#qiime2-01-import-data-paired.cwl/make_import_directory/forward_sequences"
},
{
"source": "#qiime2-01-import-data-paired.cwl/reverse_sequences",
"id": "#qiime2-01-import-data-paired.cwl/make_import_directory/reverse_sequences"
}
],
"out": [
"#qiime2-01-import-data-paired.cwl/make_import_directory/dir"
],
"id": "#qiime2-01-import-data-paired.cwl/make_import_directory"
},
{
"run": "#tools-import.cwl",
"in": [
{
"source": "#qiime2-01-import-data-paired.cwl/make_import_directory/dir",
"id": "#qiime2-01-import-data-paired.cwl/make_sequences_artifact/input_path"
},
{
"source": "#qiime2-01-import-data-paired.cwl/sequences_artifact_filename",
"id": "#qiime2-01-import-data-paired.cwl/make_sequences_artifact/output_filename"
},
{
"source": "#qiime2-01-import-data-paired.cwl/sequences_artifact_type",
"id": "#qiime2-01-import-data-paired.cwl/make_sequences_artifact/type"
}
],
"out": [
"#qiime2-01-import-data-paired.cwl/make_sequences_artifact/sequences_artifact"
],
"id": "#qiime2-01-import-data-paired.cwl/make_sequences_artifact"
}
],
"id": "#qiime2-01-import-data-paired.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"label": "qiime2 demux paired sequences",
"inputs": [
{
"type": "string",
"default": "demux.qza",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_sequences_filename"
},
{
"type": "string",
"default": "demux.qzv",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_visualization_filename"
},
{
"type": "string",
"id": "#qiime2-02-demux-emp-paired.cwl/metadata_barcodes_column"
},
{
"type": "boolean",
"default": true,
"id": "#qiime2-02-demux-emp-paired.cwl/rev_comp_mapping_barcodes"
},
{
"type": "File",
"id": "#qiime2-02-demux-emp-paired.cwl/sample_metadata"
},
{
"type": "File",
"id": "#qiime2-02-demux-emp-paired.cwl/sequences_artifact"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#qiime2-02-demux-emp-paired.cwl/demux_sequences/demux_sequences_artifact",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_sequences_artifact"
},
{
"type": "File",
"outputSource": "#qiime2-02-demux-emp-paired.cwl/demux_visualization/demux_visualization_artifact",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_visualization_artifact"
}
],
"steps": [
{
"run": "#demux-emp-paired.cwl",
"in": [
{
"source": "#qiime2-02-demux-emp-paired.cwl/metadata_barcodes_column",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_sequences/barcodes_column"
},
{
"source": "#qiime2-02-demux-emp-paired.cwl/sample_metadata",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_sequences/barcodes_file"
},
{
"source": "#qiime2-02-demux-emp-paired.cwl/demux_sequences_filename",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_sequences/per_sample_sequences_filename"
},
{
"source": "#qiime2-02-demux-emp-paired.cwl/rev_comp_mapping_barcodes",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_sequences/rev_comp_mapping_barcodes"
},
{
"source": "#qiime2-02-demux-emp-paired.cwl/sequences_artifact",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_sequences/seqs"
}
],
"out": [
"#qiime2-02-demux-emp-paired.cwl/demux_sequences/demux_sequences_artifact"
],
"id": "#qiime2-02-demux-emp-paired.cwl/demux_sequences"
},
{
"run": "#demux-summarize.cwl",
"in": [
{
"source": "#qiime2-02-demux-emp-paired.cwl/demux_sequences/demux_sequences_artifact",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_visualization/data"
},
{
"source": "#qiime2-02-demux-emp-paired.cwl/demux_visualization_filename",
"id": "#qiime2-02-demux-emp-paired.cwl/demux_visualization/visualization_filename"
}
],
"out": [
"#qiime2-02-demux-emp-paired.cwl/demux_visualization/demux_visualization_artifact"
],
"id": "#qiime2-02-demux-emp-paired.cwl/demux_visualization"
}
],
"id": "#qiime2-02-demux-emp-paired.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Creates a directory populated with specifically named files as required by qiime2 EMPPairedEndSequences",
"requirements": [
{
"class": "ShellCommandRequirement"
}
],
"inputs": [
{
"type": "File",
"label": "barcode read associated with each sequence",
"id": "#EMPPairedEndSequences-directory.cwl/barcodes"
},
{
"type": "string",
"label": "Name of the resulting directory",
"default": "emp-single-end-sequences",
"id": "#EMPPairedEndSequences-directory.cwl/directory_name"
},
{
"type": "File",
"label": "forward sequence reads",
"id": "#EMPPairedEndSequences-directory.cwl/forward_sequences"
},
{
"type": "File",
"label": "reverse sequence reads",
"id": "#EMPPairedEndSequences-directory.cwl/reverse_sequences"
}
],
"arguments": [
"mkdir",
"$(inputs.directory_name)",
"&&",
"cp",
"$(inputs.forward_sequences.path)",
"$(inputs.directory_name)/forward.fastq.gz",
"&&",
"cp",
"$(inputs.reverse_sequences.path)",
"$(inputs.directory_name)/reverse.fastq.gz",
"&&",
"cp",
"$(inputs.barcodes.path)",
"$(inputs.directory_name)/barcodes.fastq.gz"
],
"outputs": [
{
"type": "Directory",
"outputBinding": {
"glob": "$(inputs.directory_name)"
},
"id": "#EMPPairedEndSequences-directory.cwl/dir"
}
],
"id": "#EMPPairedEndSequences-directory.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Demultiplex paired-end sequence data for data generated with the Earth Microbiome Project (EMP) amplicon sequencing protocol",
"hints": [
{
"class": "DockerRequirement",
"dockerPull": "qiime2/core:2018.4",
"id": "#qiime2-docker-hint.yml",
"name": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "string",
"label": "Column from metadata file or artifact viewable as metadata",
"inputBinding": {
"prefix": "--m-barcodes-column"
},
"id": "#demux-emp-paired.cwl/barcodes_column"
},
{
"type": "File",
"label": "Metadata file or artifact viewable as metadata",
"inputBinding": {
"prefix": "--m-barcodes-file"
},
"id": "#demux-emp-paired.cwl/barcodes_file"
},
{
"type": "string",
"label": "Filename for the resulting demultiplexed sequences",
"inputBinding": {
"prefix": "--o-per-sample-sequences"
},
"id": "#demux-emp-paired.cwl/per_sample_sequences_filename"
},
{
"type": "boolean",
"label": "the barcode sequences in the sample metadata will be reverse complement prior to demultiplexing",
"inputBinding": {
"prefix": "--p-rev-comp-mapping-barcodes"
},
"id": "#demux-emp-paired.cwl/rev_comp_mapping_barcodes"
},
{
"type": "File",
"label": "qiime2 artifact file with formats (EMPPairedEndSequences | EMPSingleEndSequences | RawSequences)",
"inputBinding": {
"prefix": "--i-seqs"
},
"id": "#demux-emp-paired.cwl/seqs"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.per_sample_sequences_filename)"
},
"id": "#demux-emp-paired.cwl/demux_sequences_artifact"
}
],
"baseCommand": [
"qiime",
"demux",
"emp-paired"
],
"id": "#demux-emp-paired.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Summarize counts per sample for all samples, and generate interactive positional quality plots based on `n` randomly selected sequences",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "File",
"label": "de-multiplexed sequences to be summarized",
"inputBinding": {
"prefix": "--i-data"
},
"id": "#demux-summarize.cwl/data"
},
{
"type": "string",
"label": "filename for the resulting visualization file",
"inputBinding": {
"prefix": "--o-visualization"
},
"id": "#demux-summarize.cwl/visualization_filename"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.visualization_filename)"
},
"id": "#demux-summarize.cwl/demux_visualization_artifact"
}
],
"baseCommand": [
"qiime",
"demux",
"summarize"
],
"id": "#demux-summarize.cwl"
},
{
"class": "CommandLineTool",
"label": "qiime2: Import data to create a new QIIME 2 Artifact",
"hints": [
{
"$import": "#qiime2-docker-hint.yml"
}
],
"inputs": [
{
"type": "Directory",
"label": "path to file or directory that should be imported",
"inputBinding": {
"prefix": "--input-path"
},
"id": "#tools-import.cwl/input_path"
},
{
"type": "string",
"label": "filename to use for output file (qza format)",
"inputBinding": {
"prefix": "--output-path"
},
"id": "#tools-import.cwl/output_filename"
},
{
"type": "string",
"label": "semantic type of the artifact that will be created upon importing",
"inputBinding": {
"prefix": "--type"
},
"id": "#tools-import.cwl/type"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.output_filename)"
},
"id": "#tools-import.cwl/sequences_artifact"
}
],
"baseCommand": [
"qiime",
"tools",
"import"
],
"id": "#tools-import.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"label": "QIIME2 Step 1 paired end sequences",
"doc": "QIIME2 Import and Demux Step 1 paired end sequences\n",
"inputs": [
{
"type": "File",
"doc": "barcodes associated with sequences in FASTQ format",
"id": "#main/barcodes"
},
{
"type": "File",
"doc": "paired ended forward sequence reads in FASTQ format",
"id": "#main/forward_sequences"
},
{
"type": "string",
"doc": "name of the column in sample_metadata that contains barcodes",
"id": "#main/metadata_barcodes_column"
},
{
"type": "File",
"doc": "paired ended reverse sequence reads in FASTQ format",
"id": "#main/reverse_sequences"
},
{
"type": "File",
"doc": "Sample metadata in tsv format",
"id": "#main/sample_metadata"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#main/demux/demux_sequences_artifact",
"id": "#main/demux_sequences_artifact"
},
{
"type": "File",
"outputSource": "#main/demux/demux_visualization_artifact",
"id": "#main/demux_visualization_artifact"
},
{
"type": "File",
"outputSource": "#main/import_data/sequences_artifact",
"id": "#main/sequences_artifact"
}
],
"steps": [
{
"run": "#qiime2-02-demux-emp-paired.cwl",
"in": [
{
"source": "#main/metadata_barcodes_column",
"id": "#main/demux/metadata_barcodes_column"
},
{
"source": "#main/sample_metadata",
"id": "#main/demux/sample_metadata"
},
{
"source": "#main/import_data/sequences_artifact",
"id": "#main/demux/sequences_artifact"
}
],
"out": [
"#main/demux/demux_sequences_artifact",
"#main/demux/demux_visualization_artifact"
],
"id": "#main/demux"
},
{
"run": "#qiime2-01-import-data-paired.cwl",
"in": [
{
"source": "#main/barcodes",
"id": "#main/import_data/barcodes"
},
{
"source": "#main/forward_sequences",
"id": "#main/import_data/forward_sequences"
},
{
"source": "#main/reverse_sequences",
"id": "#main/import_data/reverse_sequences"
}
],
"out": [
"#main/import_data/sequences_artifact"
],
"id": "#main/import_data"
}
],
"id": "#main"
}
]
}