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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
1.5 KiB
YAML
57 lines
1.5 KiB
YAML
name: dragonflye
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description: Assemble bacterial isolate genomes from Nanopore reads
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keywords:
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- bacterial
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- assembly
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- nanopore
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tools:
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- dragonflye:
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description: Microbial assembly pipeline for Nanopore reads
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homepage: https://github.com/rpetit3/dragonflye
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documentation: https://github.com/rpetit3/dragonflye/blob/main/README.md
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licence: ["GPL v2"]
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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: Input Nanopore FASTQ file
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pattern: "*.fastq.gz"
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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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- contigs:
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type: file
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description: The final assembly produced by Dragonflye
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pattern: "contigs.fa"
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- log:
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type: file
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description: Full log file for bug reporting
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pattern: "dragonflye.log"
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- raw_contigs:
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type: file
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description: Raw assembly produced by the assembler (Flye, Miniasm, or Raven)
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pattern: "{flye,miniasm,raven}.fasta"
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- txt:
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type: file
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description: Assembly information output by Flye
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pattern: "flye-info.txt"
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- gfa:
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type: file
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description: Assembly graph produced by Miniasm, or Raven
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pattern: "{miniasm,raven}-unpolished.gfa"
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authors:
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- "@rpetit3"
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