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906577873b
* 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>
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: "versions.yml"
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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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