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https://github.com/MillironX/nf-core_modules.git
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e745e167c1
* 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>
62 lines
1.6 KiB
YAML
62 lines
1.6 KiB
YAML
name: rseqc_junctionannotation
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description: compare detected splice junctions to reference gene model
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keywords:
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- junctions
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- splicing
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- rnaseq
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tools:
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- rseqc:
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description: |
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RSeQC package provides a number of useful modules that can comprehensively evaluate
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high throughput sequence data especially RNA-seq data.
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homepage: http://rseqc.sourceforge.net/
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documentation: http://rseqc.sourceforge.net/
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doi: 10.1093/bioinformatics/bts356
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licence: ["GPL-3.0-or-later"]
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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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- bam:
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type: file
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description: the alignment in bam format
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pattern: "*.{bam}"
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- bed:
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type: file
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description: a bed file for the reference gene model
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pattern: "*.{bed}"
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output:
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- bed:
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type: file
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description: bed file of annotated junctions
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pattern: "*.junction.bed"
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- interact_bed:
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type: file
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description: Interact bed file
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pattern: "*.Interact.bed"
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- xls:
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type: file
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description: xls file with junction information
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pattern: "*.xls"
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- pdf:
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type: file
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description: junction plot
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pattern: "*.junction.pdf"
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- events_pdf:
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type: file
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description: events plot
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pattern: "*.events.pdf"
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- rscript:
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type: file
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description: Rscript to reproduce the plots
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pattern: "*.r"
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- log:
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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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authors:
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- "@drpatelh"
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- "@kevinmenden"
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