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97 lines
2.8 KiB
YAML
97 lines
2.8 KiB
YAML
name: star_align
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description: Align reads to a reference genome using STAR
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keywords:
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- align
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- fasta
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- genome
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- reference
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tools:
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- star:
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description: |
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STAR is a software package for mapping DNA sequences against
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a large reference genome, such as the human genome.
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homepage: https://github.com/alexdobin/STAR
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manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
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doi: 10.1093/bioinformatics/bts635
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- enable_conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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- singularity_pull_docker_container:
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type: boolean
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description: |
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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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: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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type: directory
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description: STAR genome index
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pattern: "star"
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output:
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- bam:
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type: file
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description: Output BAM file containing read alignments
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pattern: "*.{bam}"
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- log_final:
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type: file
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description: STAR final log file
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pattern: "*Log.final.out"
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- log_out:
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type: file
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description: STAR lot out file
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pattern: "*Log.out"
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- log_progress:
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type: file
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description: STAR log progress file
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pattern: "*Log.progress.out"
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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_sorted:
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type: file
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description: Sorted BAM file of read alignments (optional)
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pattern: "*sortedByCoord.out.bam"
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- bam_transcript:
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type: file
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description: Output BAM file of transcriptome alignment (optional)
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pattern: "*toTranscriptome.out.bam"
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- bam_unsorted:
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type: file
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description: Unsorted BAM file of read alignments (optional)
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pattern: "*Aligned.unsort.out.bam"
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- fastq:
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type: file
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description: Unmapped FastQ files (optional)
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pattern: "*fastq.gz"
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- tab:
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type: file
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description: STAR output tab file(s) (optional)
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pattern: "*.tab"
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authors:
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- "@kevinmenden"
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- "@drpatelh"
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