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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>
84 lines
2.3 KiB
YAML
84 lines
2.3 KiB
YAML
name: spades
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description: Assembles a small genome (bacterial, fungal, viral)
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keywords:
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- genome
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- assembly
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- genome assembler
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- small genome
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- de novo assembler
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tools:
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- spades:
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description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
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homepage: http://cab.spbu.ru/files/release3.15.0/manual.html
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documentation: http://cab.spbu.ru/files/release3.15.0/manual.html
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tool_dev_url: https://github.com/ablab/spades
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doi: 10.1089/cmb.2012.0021
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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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- illumina:
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type: file
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description: |
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List of input FastQ (Illumina or PacBio CCS reads) files
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of size 1 and 2 for single-end and paired-end data,
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respectively. This input data type is required.
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- pacbio:
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type: file
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description: |
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List of input PacBio CLR FastQ files of size 1.
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- nanopore:
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type: file
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description: |
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List of input FastQ files of size 1, originating from Oxford Nanopore technology.
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- hmm:
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type: file
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description: File or directory with amino acid HMMs for Spades HMM-guided mode.
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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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- scaffolds:
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type: file
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description: |
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Fasta file containing scaffolds
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pattern: "*.fa.gz"
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- contigs:
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type: file
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description: |
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Fasta file containing contigs
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pattern: "*.fa.gz"
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- transcripts:
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type: file
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description: |
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Fasta file containing transcripts
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pattern: "*.fa.gz"
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- gene_clusters:
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type: file
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description: |
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Fasta file containing gene_clusters
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pattern: "*.fa.gz"
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- gfa:
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type: file
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description: |
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gfa file containing assembly
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pattern: "*.gfa.gz"
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- log:
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type: file
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description: |
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Spades log file
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pattern: "*.log"
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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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authors:
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- "@JoseEspinosa"
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- "@drpatelh"
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- "@d4straub"
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