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nf-core_modules/modules/malt/build/meta.yml

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module: MALT/BUILD (#645) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start MALT-build * Start MALT build (missing meta files and outputs specS) * Local tests * Correct test map_type * Finished module, just waiting for UNZIP module to finalise tests * Correct tests in preparation for Unzip * Ouptut log file too * Update meta.yml * Rename log file * Rename log file * Remove debugging stuff * Add Unzip module * Linting update * Linting update * Fix input db * Fix db file in cmd * Update modules/malt/build/main.nf * Update modules/malt/build/main.nf * Update main.nf
2021-08-03 14:24:19 +00:00
name: malt_build
description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
keywords:
- malt
- alignment
- metagenomics
- ancient DNA
- aDNA
- palaeogenomics
- archaeogenomics
- microbiome
- database
tools:
- malt:
description: A tool for mapping metagenomic data
homepage: https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
tool_dev_url: None
doi: "10.1038/s41559-017-0446-6"
Fix formatting in yaml files, add yamllint config (#1279) * 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>
2022-02-15 11:15:27 +00:00
licence: ["GPL v3"]
module: MALT/BUILD (#645) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start MALT-build * Start MALT build (missing meta files and outputs specS) * Local tests * Correct test map_type * Finished module, just waiting for UNZIP module to finalise tests * Correct tests in preparation for Unzip * Ouptut log file too * Update meta.yml * Rename log file * Rename log file * Remove debugging stuff * Add Unzip module * Linting update * Linting update * Fix input db * Fix db file in cmd * Update modules/malt/build/main.nf * Update modules/malt/build/main.nf * Update main.nf
2021-08-03 14:24:19 +00:00
input:
- fastas:
type: file
description: Directory of, or FASTA reference files for indexing
pattern: "*/|*.fasta"
- seq_type:
type: string
description: Type of input data
pattern: "DNA|Protein"
- gff:
type: file
description: Directory of, or GFF3 files of input FASTA files
pattern: "*/|*.gff|*.gff3"
- map_db:
type: file
description: MEGAN .db file from https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html
pattern:
output:
Update versions key in meta.yml for all modules (#787)
2021-10-03 07:20:26 +00:00
- versions:
module: MALT/BUILD (#645) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start MALT-build * Start MALT build (missing meta files and outputs specS) * Local tests * Correct test map_type * Finished module, just waiting for UNZIP module to finalise tests * Correct tests in preparation for Unzip * Ouptut log file too * Update meta.yml * Rename log file * Rename log file * Remove debugging stuff * Add Unzip module * Linting update * Linting update * Fix input db * Fix db file in cmd * Update modules/malt/build/main.nf * Update modules/malt/build/main.nf * Update main.nf
2021-08-03 14:24:19 +00:00
type: file
Update versions key in meta.yml for all modules (#787)
2021-10-03 07:20:26 +00:00
description: File containing software versions
Bulk update modules to use versions.yml (#739) * New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 08:41:24 +00:00
pattern: "versions.yml"
module: MALT/BUILD (#645) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start MALT-build * Start MALT build (missing meta files and outputs specS) * Local tests * Correct test map_type * Finished module, just waiting for UNZIP module to finalise tests * Correct tests in preparation for Unzip * Ouptut log file too * Update meta.yml * Rename log file * Rename log file * Remove debugging stuff * Add Unzip module * Linting update * Linting update * Fix input db * Fix db file in cmd * Update modules/malt/build/main.nf * Update modules/malt/build/main.nf * Update main.nf
2021-08-03 14:24:19 +00:00
- index:
type: directory
description: Directory containing MALT database index directory
pattern: "malt_index/"
- log:
type: file
description: Log file from STD out of malt-build
pattern: "malt-build.log"
authors:
- "@jfy133"
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