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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
63 lines
1.7 KiB
YAML
63 lines
1.7 KiB
YAML
name: rsem_calculateexpression
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description: Calculate expression with RSEM
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keywords:
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- rsem
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- expression
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- quantification
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tools:
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- rseqc:
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description: |
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
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homepage: https://github.com/deweylab/RSEM
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documentation: https://github.com/deweylab/RSEM
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doi: https://doi.org/10.1186/1471-2105-12-323
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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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- reads:
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type: file
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description: Input reads for quantification
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pattern: "*.fastq.gz"#
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- index:
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type: file
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description: RSEM index
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pattern: "rsem/*"
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output:
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- counts_gene:
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type: file
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description: Expression counts on gene level
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pattern: "*.genes.results"
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- counts_transctips:
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type: file
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description: Expression counts on transcript level
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pattern: "*.isoforms.results"
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- stat:
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type: file
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description: RSEM statistics
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pattern: "*.stat"
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- logs:
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type: file
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description: RSEM logs
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pattern: "*.log"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- bam_star:
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type: file
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description: BAM file generated by STAR (optional)
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pattern: "*.STAR.genome.bam"
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- bam_genome:
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type: file
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description: Genome BAM file (optional)
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pattern: "*.genome.bam"
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- bam_transcript:
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type: file
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description: Transcript BAM file (optional)
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pattern: "*.transcript.bam"
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authors:
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- "@drpatelh"
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- "@kevinmenden"
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