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3531824af8
* Update DIAMOND module to output log file * Updating DIAMOND module to output log file - with jfy133 suggestions Co-authored-by: Mahwash Jamy <mahwashjamy@n183-p186.eduroam.kth.se> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
81 lines
2.3 KiB
YAML
81 lines
2.3 KiB
YAML
name: diamond_blastx
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description: Queries a DIAMOND database using blastx mode
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keywords:
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- fasta
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- diamond
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- blastx
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- DNA sequence
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tools:
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- diamond:
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description: Accelerated BLAST compatible local sequence aligner
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homepage: https://github.com/bbuchfink/diamond
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documentation: https://github.com/bbuchfink/diamond/wiki
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tool_dev_url: https://github.com/bbuchfink/diamond
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doi: "doi:10.1038/s41592-021-01101-x"
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licence: ["GPL v3.0"]
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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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- fasta:
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type: file
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description: Input fasta file containing query sequences
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pattern: "*.{fa,fasta}"
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- db:
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type: directory
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description: Directory containing the nucelotide blast database
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pattern: "*"
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- out_ext:
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type: string
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description: |
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Specify the type of output file to be generated. `blast` corresponds to
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BLAST pairwise format. `xml` corresponds to BLAST xml format.
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`txt` corresponds to to BLAST tabular format. `tsv` corresponds to
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taxonomic classification format.
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pattern: "blast|xml|txt|daa|sam|tsv|paf"
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output:
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- blast:
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type: file
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description: File containing blastp hits
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pattern: "*.{blast}"
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- xml:
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type: file
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description: File containing blastp hits
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pattern: "*.{xml}"
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- txt:
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type: file
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description: File containing hits in tabular BLAST format.
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pattern: "*.{txt}"
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- daa:
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type: file
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description: File containing hits DAA format
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pattern: "*.{daa}"
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- sam:
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type: file
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description: File containing aligned reads in SAM format
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pattern: "*.{sam}"
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- tsv:
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type: file
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description: Tab separated file containing taxonomic classification of hits
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pattern: "*.{tsv}"
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- paf:
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type: file
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description: File containing aligned reads in pairwise mapping format format
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pattern: "*.{paf}"
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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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- log:
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type: file
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description: Log file containing stdout information
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pattern: "*.{log}"
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authors:
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- "@spficklin"
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- "@jfy133"
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- "@mjamy"
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