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    "annotation": "This workflow performs contamination cleaning steps on assembled genomes. Users specify an input genome (fasta/fasta.gz) and taxonomic information corresponding to the source organism. There are two screening steps for foreign organism sequences (FCS-GX) and adaptors (FCS-adaptor), each followed by a cleaning step to remove identified contaminants. The final output is a cleaned genome. ",
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    "creator": [
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            "class": "Organization",
            "name": "National Center for Biotechnology Information",
            "url": "https://github.com/ncbi/fcs"
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    "format-version": "0.1",
    "license": "http://www.usa.gov/publicdomain/label/1.0/",
    "name": "NCBI Foreign Contamination Screen",
    "steps": {
        "0": {
            "annotation": "input must be an assembled genome in fasta/fasta.gz format. FCS is not intended to identify contaminants in sequencing reads inputs.",
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                    "description": "input must be an assembled genome in fasta/fasta.gz format. FCS is not intended to identify contaminants in sequencing reads inputs.",
                    "name": "Input genome"
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                    "name": "mode"
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            "label": "FCS-GX screen",
            "name": "NCBI FCS GX",
            "outputs": [
                {
                    "name": "taxonomy_report",
                    "type": "tabular"
                },
                {
                    "name": "action_report",
                    "type": "tabular"
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                    "uuid": "9741edf2-4be6-45a3-980d-99b1aea18380"
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                    "description": "runtime parameter for tool NCBI FCS GX",
                    "name": "mode"
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                {
                    "description": "runtime parameter for tool NCBI FCS GX",
                    "name": "mode"
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            ],
            "label": "FCS-GX clean",
            "name": "NCBI FCS GX",
            "outputs": [
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                    "name": "contam_fasta",
                    "type": "fasta"
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                    "name": "clean_fasta",
                    "type": "fasta"
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                    "output_name": "clean_fasta"
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            "label": "FCS-adaptor screen",
            "name": "NCBI FCS Adaptor",
            "outputs": [
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                    "name": "adaptor_report",
                    "type": "tabular"
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                    "name": "clean_fasta",
                    "type": "fasta"
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            "workflow_outputs": [
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                    "output_name": "adaptor_report",
                    "uuid": "6a4baf46-80b0-4a96-b864-9201fc80cdb7"
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                {
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                    "uuid": "1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb"
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            "inputs": [
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                    "description": "runtime parameter for tool NCBI FCS GX",
                    "name": "mode"
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            "label": "FCS-adaptor clean",
            "name": "NCBI FCS GX",
            "outputs": [
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                    "name": "contam_fasta",
                    "type": "fasta"
                },
                {
                    "name": "clean_fasta",
                    "type": "fasta"
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    "tags": [
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}