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b6ed584443
* Add saving of stderr output as a log file as it contains summary statistics * Apply suggestions from code review
65 lines
1.9 KiB
YAML
65 lines
1.9 KiB
YAML
name: "motus_profile"
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description: Taxonomic meta-omics profiling using universal marker genes
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keywords:
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- classify
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- metagenomics
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- fastq
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- taxonomic profiling
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tools:
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- "motus":
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description: "Marker gene-based OTU (mOTU) profiling"
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homepage: "https://motu-tool.org/"
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documentation: "https://github.com/motu-tool/mOTUs/wiki"
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tool_dev_url: "https://github.com/motu-tool/mOTUs"
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doi: "10.1038/s41467-019-08844-4"
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licence: "['GPL v3']"
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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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- reads:
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type: file
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description: |
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List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
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respectively.
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Or the intermediate bam file mapped by bwa to the mOTUs database or
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the output bam file from motus profile.
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Or the intermediate mgc read counts table.
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pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}"
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- db:
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type: directory
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description: |
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mOTUs database downloaded by `motus downloadDB`
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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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- out:
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type: file
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description: Results with taxonomic classification of each read
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pattern: "*.out"
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- bam:
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type: file
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description: Optional intermediate sorted BAM file from BWA
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pattern: "*.{bam}"
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- mgc:
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type: file
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description: Optional intermediate mgc read count table file saved with `-M`.
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pattern: "*.{mgc}"
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- log:
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type: file
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description: Standard error logging file containing summary statistics
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pattern: "*.log"
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authors:
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- "@jianhong"
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