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bd0fa881f6
* changing mv by gzip * changing mv by gzip * first module creation * add test.yml * add flye to pyestes_modules.yml * update flye module * delete functions.nf * generate test.yml * fix contains from test.yml * test file assembly_info.txt with regex * check that file contains at least contig_1 * fix typo in contains * update version * split fastq file for raw runs * use asm-coverage to reduce memory usage * fix module name error * add genome-size * decrease coverage * change test data for raw runs * add coverage and genome size * Apply comments from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * after many trys, add a stub run * remove md5sum for stub run * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix review comments * Apply suggestions from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * no hardcoded version in stub run * Update modules/flye/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
69 lines
1.9 KiB
YAML
69 lines
1.9 KiB
YAML
name: "flye"
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description: De novo assembler for single molecule sequencing reads
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keywords:
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- assembly
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- genome
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- de novo
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- genome assembler
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- single molecule
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tools:
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- "flye":
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description: "Fast and accurate de novo assembler for single molecule sequencing reads"
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homepage: "https://github.com/fenderglass/Flye"
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documentation: "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md"
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tool_dev_url: "https://github.com/fenderglass/Flye"
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doi: "10.1038/s41592-020-00971-x"
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licence: "['BSD-3-clause']"
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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' ]
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- reads:
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type: file
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description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format.
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pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}"
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- mode:
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type: value
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description: Flye mode depending on the input data (source and error rate)
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pattern: "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq"
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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' ]
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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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- fasta:
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type: file
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description: Assembled FASTA file
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pattern: "*.fasta.gz"
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- gfa:
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type: file
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description: Repeat graph in gfa format
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pattern: "*.gfa.gz"
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- gv:
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type: file
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description: Repeat graph in gv format
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pattern: "*.gv.gz"
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- txt:
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type: file
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description: Extra information and statistics about resulting contigs
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pattern: "*.txt"
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- log:
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type: file
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description: Flye log file
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pattern: "*.log"
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- json:
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type: file
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description: Flye parameters
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pattern: "*.json"
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authors:
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- "@mirpedrol"
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