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f1c5384c31
* fix: remove left-over unnecessary code * Add prinseq++ * Remove last todo * Fix tests due to variability of output FASTQs (reads can be ordered differently between runs) * Apply suggestions from code review
60 lines
1.8 KiB
YAML
60 lines
1.8 KiB
YAML
name: "prinseqplusplus"
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description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data
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keywords:
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- fastq
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- fasta
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- filter
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- trim
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tools:
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- "prinseqplusplus":
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description: "PRINSEQ++ - Multi-threaded C++ sequence cleaning"
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homepage: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
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documentation: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
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tool_dev_url: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
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doi: "10.7287/peerj.preprints.27553v1"
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licence: "['GPL v2']"
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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
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data, respectively.
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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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- good_reads:
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type: file
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description: Reads passing filter(s) in gzipped FASTQ format
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pattern: "*_good_out_{R1,R2}.fastq.gz"
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- single_reads:
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type: file
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description: |
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Single reads without the pair passing filter(s) in gzipped FASTQ format
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pattern: "*_single_out_{R1,R2}.fastq.gz"
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- bad_reads:
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type: file
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description: |
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Reads without not passing filter(s) in gzipped FASTQ format
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pattern: "*_bad_out_{R1,R2}.fastq.gz"
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- log:
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type: file
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description: |
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Verbose level 2 STDOUT information in a log file
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pattern: "*.log"
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authors:
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- "@jfy133"
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