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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>
53 lines
1.7 KiB
YAML
53 lines
1.7 KiB
YAML
name: samblaster
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description: |
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This module combines samtools and samblaster in order to use
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samblaster capability to filter or tag SAM files, with the advantage
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of maintaining both input and output in BAM format.
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Samblaster input must contain a sequence header: for this reason it has been piped
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with the "samtools view -h" command.
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Additional desired arguments for samtools can be passed using:
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options.args2 for the input bam file
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options.args3 for the output bam file
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keywords:
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- sort
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tools:
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- samblaster:
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description: |
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samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files.
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It can also optionally output discordant read pairs and/or split read mappings to separate SAM files,
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and/or unmapped/clipped reads to a separate FASTQ file.
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By default, samblaster reads SAM input from stdin and writes SAM to stdout.
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homepage: None
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documentation: https://github.com/GregoryFaust/samblaster
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tool_dev_url: https://github.com/GregoryFaust/samblaster
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doi: "10.1093/bioinformatics/btu314"
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licence: ["MIT"]
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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: BAM file
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pattern: "*.bam"
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output:
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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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- 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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- bam:
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type: file
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description: Tagged or filtered BAM file
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pattern: "*.bam"
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authors:
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- "@lescai"
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