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* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
62 lines
2 KiB
YAML
62 lines
2 KiB
YAML
name: megahit
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description: An ultra-fast metagenomic assembler for large and complex metagenomics
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keywords:
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- megahit
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- denovo
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- assembly
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- debruijn
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- metagenomics
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tools:
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- megahit:
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description: "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"
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homepage: https://github.com/voutcn/megahit
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documentation: https://github.com/voutcn/megahit
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tool_dev_url: https://github.com/voutcn/megahit
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doi: "10.1093/bioinformatics/btv033"
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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 and input single, or paired-end FASTA/FASTQ files (optionally decompressed)
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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 files of size 1 and 2 for single-end and paired-end data,
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respectively in gzipped or uncompressed FASTQ or FASTA format.
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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: Final final contigs result of the assembly in FASTA format.
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pattern: "*.contigs.fa.gz"
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- k_contigs:
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type: file
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description: Contigs assembled from the de Bruijn graph of order-K
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pattern: "k*.contigs.fa.gz"
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- addi_contigs:
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type: file
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description: Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K
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pattern: "k*.addi.fa.gz"
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- local_contigs:
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type: file
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description: Contigs of the locally assembled contigs for k=K
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pattern: "k*.local.fa.gz"
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- kfinal_contigs:
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type: file
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description: Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty
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pattern: "k*.final.contigs.fa.gz"
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authors:
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- "@jfy133"
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