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62 lines
1.9 KiB
YAML
Generated
62 lines
1.9 KiB
YAML
Generated
name: samtools_fastq
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description: Converts a SAM/BAM/CRAM file to FASTQ
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keywords:
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- bam
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- sam
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- cram
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- fastq
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: http://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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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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- input:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- interleave:
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type: boolean
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description: Set true for interleaved fastq file
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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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- fastq:
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type: file
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description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.
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pattern: "*_{1,2}.fastq.gz"
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- interleaved:
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type: file
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description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
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pattern: "*_interleaved.fastq.gz"
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- singleton:
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type: file
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description: Compressed FASTQ file with singleton reads
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pattern: "*_singleton.fastq.gz"
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- other:
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type: file
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description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset
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pattern: "*_other.fastq.gz"
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authors:
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- "@priyanka-surana"
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- "@suzannejin"
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