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90 lines
3 KiB
YAML
Generated
90 lines
3 KiB
YAML
Generated
name: adapterremoval
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description: Trim sequencing adapters and collapse overlapping reads
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keywords:
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- trimming
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- adapters
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- merging
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- fastq
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tools:
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- adapterremoval:
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description: The AdapterRemoval v2 tool for merging and clipping reads.
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homepage: https://github.com/MikkelSchubert/adapterremoval
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documentation: https://adapterremoval.readthedocs.io
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licence: ["GPL v3"]
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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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pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
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- adapterlist:
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type: file
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description: Optional text file containing list of adapters to look for for removal
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with one adapter per line. Otherwise will look for default adapters (see
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AdapterRemoval man page), or can be modified to remove user-specified
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adapters via ext.args.
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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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- singles_truncated:
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type: file
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description: |
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Adapter trimmed FastQ files of either single-end reads, or singleton
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'orphaned' reads from merging of paired-end data (i.e., one of the pair
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was lost due to filtering thresholds).
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pattern: "*.truncated.fastq.gz"
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- discarded:
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type: file
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description: |
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Adapter trimmed FastQ files of reads that did not pass filtering
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thresholds.
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pattern: "*.discarded.fastq.gz"
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- pair1_truncated:
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type: file
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description: |
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Adapter trimmed R1 FastQ files of paired-end reads that did not merge
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with their respective R2 pair due to long templates. The respective pair
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is stored in 'pair2_truncated'.
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pattern: "*.pair1.truncated.fastq.gz"
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- pair2_truncated:
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type: file
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description: |
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Adapter trimmed R2 FastQ files of paired-end reads that did not merge
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with their respective R1 pair due to long templates. The respective pair
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is stored in 'pair1_truncated'.
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pattern: "*.pair2.truncated.fastq.gz"
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- collapsed:
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type: file
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description: |
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Collapsed FastQ of paired-end reads that successfully merged with their
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respective R1 pair but were not trimmed.
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pattern: "*.collapsed.fastq.gz"
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- collapsed_truncated:
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type: file
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description: |
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Collapsed FastQ of paired-end reads that successfully merged with their
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respective R1 pair and were trimmed of adapter due to sufficient overlap.
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pattern: "*.collapsed.truncated.fastq.gz"
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- log:
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type: file
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description: AdapterRemoval log file
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pattern: "*.settings"
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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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- "@maxibor"
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- "@jfy133"
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