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63 lines
1.9 KiB
YAML
63 lines
1.9 KiB
YAML
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name: "fcs_fcsadaptor"
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description: Run NCBI's FCS adaptor on assembled genomes
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keywords:
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- assembly
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- genomics
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- quality control
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- contamination
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- NCBI
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tools:
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- "fcs":
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description: |
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The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign
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organisms in genome assemblies to prepare your data for submission. Therefore, the
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submission process to NCBI is faster and fewer contaminated genomes are submitted.
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This reduces errors in analyses and conclusions, not just for the original data submitter
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but for all subsequent users of the assembly.
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homepage: "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/"
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documentation: "https://github.com/ncbi/fcs/wiki/FCS-adaptor"
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tool_dev_url: "https://github.com/ncbi/fcs"
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doi: ""
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licence: "United States Government Work"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- assembly:
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type: file
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description: assembly fasta file
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- cleaned_assembly:
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type: file
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description: Cleaned assembly in fasta format
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pattern: "*.{cleaned_sequences.fa.gz}"
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- adaptor_report:
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type: file
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description: Report of identified adaptors
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pattern: "*.{fcs_adaptor_report.txt}"
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- log:
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type: file
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description: Log file
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pattern: "*.{fcs_adaptor.log}"
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- pipeline_args:
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type: file
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description: Run arguments
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pattern: "*.{pipeline_args.yaml}"
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- skipped_trims:
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type: file
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description: Skipped trim information
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pattern: "*.{skipped_trims.jsonl}"
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authors:
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- "@d4straub"
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