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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 * Added, just need to finish tests once we have bacterial data * Add prelim test data * Fix version reporting * Add tests based on proposed test-dataset * Finalise new testdata * Fix md5sum issue by removing it... * Update main.nf * 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>
79 lines
2.5 KiB
YAML
79 lines
2.5 KiB
YAML
name: maxbin2
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description: MaxBin is a software that is capable of clustering metagenomic contigs
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keywords:
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- metagenomics
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- assembly
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- binning
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- maxbin2
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- de novo assembly
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- mags
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- metagenome-assembled genomes
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- contigs
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tools:
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- maxbin2:
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description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
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homepage: https://sourceforge.net/projects/maxbin/
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documentation: https://sourceforge.net/projects/maxbin/
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tool_dev_url: https://sourceforge.net/projects/maxbin/
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doi: "10.1093/bioinformatics/btv638"
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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', single_end:false ]
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- contigs:
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type: file
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description: Multi FASTA file containing assembled contigs of a given sample
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pattern: "*.fasta"
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- reads:
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type: file
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description: Reads used to assemble contigs in FASTA or FASTQ format. Do not supply at the same time as abundance files.
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pattern: "*.fasta"
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- abund:
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type: file
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description: Contig abundance files, i.e. reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files.
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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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- binned_fastas:
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type: file
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description: Binned contigs, one per bin designated with numeric IDs
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pattern: "*.fasta.gz"
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- summary:
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type: file
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description: Summary file describing which contigs are being classified into which bin
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pattern: "*.summary"
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- log:
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type: file
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description: Log file recording the core steps of MaxBin algorithm
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pattern: "*.log.gz"
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- marker:
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type: file
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description: Marker gene presence numbers for each bin
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pattern: "*.marker.gz"
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- unbinned_fasta:
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type: file
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description: All sequences that pass the minimum length threshold but are not classified successfully.
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pattern: "*.noclass.gz"
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- tooshort_fasta:
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type: file
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description: All sequences that do not meet the minimum length threshold.
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pattern: "*.tooshort.gz"
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- marker_genes:
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type: file
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description: All sequences that do not meet the minimum length threshold.
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pattern: "*.marker_of_each_gene.tar.gz"
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authors:
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- "@jfy133"
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