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59 lines
2.4 KiB
YAML
59 lines
2.4 KiB
YAML
name: metaphlan3_metaphlan3
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description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
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keywords:
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- metagenomics
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- classification
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- fastq
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- bam
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- fasta
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tools:
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- metaphlan3:
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description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance
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homepage: https://huttenhower.sph.harvard.edu/metaphlan/
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documentation: https://github.com/biobakery/MetaPhlAn
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doi: "10.7554/eLife.65088"
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licence: ["MIT License"]
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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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- input:
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type: file
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description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out)
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pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}"
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- metaphlan_db:
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type: file
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description: |
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Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/.
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Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3!
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pattern: "*/"
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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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- profile:
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type: file
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description: Tab-separated output file of the predicted taxon relative abundances
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pattern: "*.{txt}"
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- biom:
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type: file
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description: General-use format for representing biological sample by observation contingency tables
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pattern: "*.{biom}"
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- bowtie2out:
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type: file
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description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 )
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pattern: "*.{bowtie2out.txt}"
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authors:
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- "@MGordon09"
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