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482 lines
18 KiB
YAML
482 lines
18 KiB
YAML
name: cutadapt
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description: |
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Cutadapt removes adapter sequences from high-throughput sequencing reads.
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keywords: [RNA-seq, scRNA-seq, high-throughput]
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links:
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homepage: https://cutadapt.readthedocs.io
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documentation: https://cutadapt.readthedocs.io
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repository: https://github.com/marcelm/cutadapt
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references:
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doi: 10.14806/ej.17.1.200
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license: MIT
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argument_groups:
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####################################################################
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- name: Specify Adapters for R1
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arguments:
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- name: --adapter
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alternatives: [-a]
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type: string
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multiple: true
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description: |
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Sequence of an adapter ligated to the 3' end (paired data:
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of the first read). The adapter and subsequent bases are
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trimmed. If a '$' character is appended ('anchoring'), the
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adapter is only found if it is a suffix of the read.
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required: false
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- name: --front
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alternatives: [-g]
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type: string
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multiple: true
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description: |
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Sequence of an adapter ligated to the 5' end (paired data:
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of the first read). The adapter and any preceding bases
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are trimmed. Partial matches at the 5' end are allowed. If
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a '^' character is prepended ('anchoring'), the adapter is
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only found if it is a prefix of the read.
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required: false
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- name: --anywhere
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alternatives: [-b]
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type: string
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multiple: true
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description: |
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Sequence of an adapter that may be ligated to the 5' or 3'
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end (paired data: of the first read). Both types of
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matches as described under -a and -g are allowed. If the
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first base of the read is part of the match, the behavior
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is as with -g, otherwise as with -a. This option is mostly
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for rescuing failed library preparations - do not use if
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you know which end your adapter was ligated to!
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required: false
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####################################################################
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- name: Specify Adapters using Fasta files for R1
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arguments:
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- name: --adapter_fasta
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type: file
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multiple: true
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description: |
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Fasta file containing sequences of an adapter ligated to the 3' end (paired data:
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of the first read). The adapter and subsequent bases are
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trimmed. If a '$' character is appended ('anchoring'), the
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adapter is only found if it is a suffix of the read.
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required: false
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- name: --front_fasta
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type: file
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description: |
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Fasta file containing sequences of an adapter ligated to the 5' end (paired data:
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of the first read). The adapter and any preceding bases
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are trimmed. Partial matches at the 5' end are allowed. If
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a '^' character is prepended ('anchoring'), the adapter is
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only found if it is a prefix of the read.
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required: false
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- name: --anywhere_fasta
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type: file
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description: |
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Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'
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end (paired data: of the first read). Both types of
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matches as described under -a and -g are allowed. If the
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first base of the read is part of the match, the behavior
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is as with -g, otherwise as with -a. This option is mostly
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for rescuing failed library preparations - do not use if
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you know which end your adapter was ligated to!
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required: false
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####################################################################
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- name: Specify Adapters for R2
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arguments:
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- name: --adapter_r2
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alternatives: [-A]
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type: string
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multiple: true
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description: |
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Sequence of an adapter ligated to the 3' end (paired data:
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of the first read). The adapter and subsequent bases are
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trimmed. If a '$' character is appended ('anchoring'), the
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adapter is only found if it is a suffix of the read.
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required: false
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- name: --front_r2
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alternatives: [-G]
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type: string
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multiple: true
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description: |
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Sequence of an adapter ligated to the 5' end (paired data:
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of the first read). The adapter and any preceding bases
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are trimmed. Partial matches at the 5' end are allowed. If
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a '^' character is prepended ('anchoring'), the adapter is
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only found if it is a prefix of the read.
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required: false
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- name: --anywhere_r2
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alternatives: [-B]
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type: string
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multiple: true
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description: |
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Sequence of an adapter that may be ligated to the 5' or 3'
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end (paired data: of the first read). Both types of
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matches as described under -a and -g are allowed. If the
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first base of the read is part of the match, the behavior
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is as with -g, otherwise as with -a. This option is mostly
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for rescuing failed library preparations - do not use if
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you know which end your adapter was ligated to!
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required: false
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####################################################################
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- name: Specify Adapters using Fasta files for R2
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arguments:
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- name: --adapter_r2_fasta
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type: file
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description: |
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Fasta file containing sequences of an adapter ligated to the 3' end (paired data:
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of the first read). The adapter and subsequent bases are
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trimmed. If a '$' character is appended ('anchoring'), the
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adapter is only found if it is a suffix of the read.
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required: false
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- name: --front_r2_fasta
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type: file
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description: |
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Fasta file containing sequences of an adapter ligated to the 5' end (paired data:
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of the first read). The adapter and any preceding bases
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are trimmed. Partial matches at the 5' end are allowed. If
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a '^' character is prepended ('anchoring'), the adapter is
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only found if it is a prefix of the read.
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required: false
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- name: --anywhere_r2_fasta
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type: file
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description: |
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Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'
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end (paired data: of the first read). Both types of
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matches as described under -a and -g are allowed. If the
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first base of the read is part of the match, the behavior
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is as with -g, otherwise as with -a. This option is mostly
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for rescuing failed library preparations - do not use if
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you know which end your adapter was ligated to!
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required: false
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####################################################################
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- name: Paired-end options
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arguments:
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- name: --pair_adapters
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type: boolean_true
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description: |
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Treat adapters given with -a/-A etc. as pairs. Either both
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or none are removed from each read pair.
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- name: --pair_filter
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type: string
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choices: [any, both, first]
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description: |
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Which of the reads in a paired-end read have to match the
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filtering criterion in order for the pair to be filtered.
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- name: --interleaved
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type: boolean_true
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description: |
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Read and/or write interleaved paired-end reads.
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####################################################################
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- name: Input parameters
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arguments:
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- name: --input
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type: file
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required: true
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description: |
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Input fastq file for single-end reads or R1 for paired-end reads.
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- name: --input_r2
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type: file
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required: false
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description: |
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Input fastq file for R2 in the case of paired-end reads.
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- name: --error_rate
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alternatives: [-E, --errors]
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type: double
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description: |
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Maximum allowed error rate (if 0 <= E < 1), or absolute
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number of errors for full-length adapter match (if E is an
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integer >= 1). Error rate = no. of errors divided by
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length of matching region. Default: 0.1 (10%).
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example: 0.1
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- name: --no_indels
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type: boolean_false
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description: |
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Allow only mismatches in alignments.
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- name: --times
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type: integer
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alternatives: [-n]
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description: |
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Remove up to COUNT adapters from each read. Default: 1.
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example: 1
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- name: --overlap
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alternatives: [-O]
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type: integer
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description: |
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Require MINLENGTH overlap between read and adapter for an
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adapter to be found. The default is 3.
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example: 3
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- name: --match_read_wildcards
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type: boolean_true
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description: |
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Interpret IUPAC wildcards in reads.
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- name: --no_match_adapter_wildcards
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type: boolean_false
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description: |
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Do not interpret IUPAC wildcards in adapters.
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- name: --action
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type: string
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choices:
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- trim
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- retain
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- mask
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- lowercase
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- none
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description: |
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What to do if a match was found. trim: trim adapter and
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up- or downstream sequence; retain: trim, but retain
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adapter; mask: replace with 'N' characters; lowercase:
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convert to lowercase; none: leave unchanged.
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The default is trim.
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example: trim
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- name: --revcomp
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alternatives: [--rc]
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type: boolean_true
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description: |
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Check both the read and its reverse complement for adapter
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matches. If match is on reverse-complemented version,
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output that one.
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####################################################################
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- name: "Demultiplexing options"
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arguments:
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- name: "--demultiplex_mode"
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type: string
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choices: ["single", "unique_dual", "combinatorial_dual"]
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required: false
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description: |
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Enable demultiplexing and set the mode for it.
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With mode 'unique_dual', adapters from the first and second read are used,
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and the indexes from the reads are only used in pairs. This implies
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--pair_adapters.
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Enabling mode 'combinatorial_dual' allows all combinations of the sets of indexes
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on R1 and R2. It is necessary to write each read pair to an output
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file depending on the adapters found on both R1 and R2.
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Mode 'single', uses indexes or barcodes located at the 5'
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end of the R1 read (single).
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####################################################################
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- name: Read modifications
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arguments:
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- name: --cut
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alternatives: [-u]
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type: integer
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multiple: true
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description: |
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Remove LEN bases from each read (or R1 if paired; use --cut_r2
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option for R2). If LEN is positive, remove bases from the
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beginning. If LEN is negative, remove bases from the end.
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Can be used twice if LENs have different signs. Applied
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*before* adapter trimming.
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- name: --cut_r2
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type: integer
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multiple: true
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description: |
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Remove LEN bases from each read (for R2). If LEN is positive, remove bases from the
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beginning. If LEN is negative, remove bases from the end.
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Can be used twice if LENs have different signs. Applied
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*before* adapter trimming.
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- name: --nextseq_trim
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type: string
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description: |
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NextSeq-specific quality trimming (each read). Trims also
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dark cycles appearing as high-quality G bases.
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- name: --quality_cutoff
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alternatives: [-q]
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type: string
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description: |
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Trim low-quality bases from 5' and/or 3' ends of each read
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before adapter removal. Applied to both reads if data is
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paired. If one value is given, only the 3' end is trimmed.
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If two comma-separated cutoffs are given, the 5' end is
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trimmed with the first cutoff, the 3' end with the second.
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- name: --quality_cutoff_r2
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alternatives: [-Q]
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type: string
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description: |
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Quality-trimming cutoff for R2. Default: same as for R1
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- name: --quality_base
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type: integer
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description: |
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Assume that quality values in FASTQ are encoded as
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ascii(quality + N). This needs to be set to 64 for some
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old Illumina FASTQ files. The default is 33.
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example: 33
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- name: --poly_a
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type: boolean_true
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description: Trim poly-A tails
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- name: --length
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alternatives: [-l]
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type: integer
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description: |
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Shorten reads to LENGTH. Positive values remove bases at
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the end while negative ones remove bases at the beginning.
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This and the following modifications are applied after
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adapter trimming.
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- name: --trim_n
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type: boolean_true
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description: Trim N's on ends of reads.
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- name: --length_tag
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type: string
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description: |
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Search for TAG followed by a decimal number in the
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description field of the read. Replace the decimal number
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with the correct length of the trimmed read. For example,
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use --length-tag 'length=' to correct fields like
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'length=123'.
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example: "length="
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- name: --strip_suffix
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type: string
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description: |
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Remove this suffix from read names if present. Can be
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given multiple times.
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- name: --prefix
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alternatives: [-x]
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type: string
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description: |
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Add this prefix to read names. Use {name} to insert the
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name of the matching adapter.
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- name: --suffix
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alternatives: [-y]
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type: string
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description: |
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Add this suffix to read names; can also include {name}
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- name: --rename
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type: string
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description: |
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Rename reads using TEMPLATE containing variables such as
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{id}, {adapter_name} etc. (see documentation)
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- name: --zero_cap
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alternatives: [-z]
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type: boolean_true
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description: Change negative quality values to zero.
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####################################################################
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- name: Filtering of processed reads
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description: |
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Filters are applied after above read modifications. Paired-end reads are
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always discarded pairwise (see also --pair_filter).
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arguments:
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- name: --minimum_length
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alternatives: [-m]
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type: string
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description: |
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Discard reads shorter than LEN. Default is 0.
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When trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately by separating them with a colon (:).
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If the colon syntax is not used, the same minimum length applies to both reads, as discussed above.
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Also, one of the values can be omitted to impose no restrictions.
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For example, with -m 17:, the length of R1 must be at least 17, but the length of R2 is ignored.
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example: "0"
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- name: --maximum_length
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alternatives: [-M]
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type: string
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description: |
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Discard reads longer than LEN. Default: no limit.
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For paired reads, see the remark for --minimum_length
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- name: --max_n
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type: string
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description: |
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Discard reads with more than COUNT 'N' bases. If COUNT is
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a number between 0 and 1, it is interpreted as a fraction
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of the read length.
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- name: --max_expected_errors
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alternatives: [--max_ee]
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type: long
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description: |
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Discard reads whose expected number of errors (computed
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from quality values) exceeds ERRORS.
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- name: --max_average_error_rate
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alternatives: [--max_aer]
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type: long
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description: |
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as --max_expected_errors (see above), but divided by
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length to account for reads of varying length.
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- name: --discard_trimmed
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alternatives: [--discard]
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type: boolean_true
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description: |
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Discard reads that contain an adapter. Use also -O to
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avoid discarding too many randomly matching reads.
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- name: --discard_untrimmed
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alternatives: [--trimmed_only]
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type: boolean_true
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description: |
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Discard reads that do not contain an adapter.
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- name: --discard_casava
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type: boolean_true
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description: |
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Discard reads that did not pass CASAVA filtering (header
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has :Y:).
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####################################################################
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- name: Output parameters
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arguments:
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- name: --report
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type: string
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choices: [full, minimal]
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description: |
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Which type of report to print: 'full' (default) or 'minimal'.
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example: full
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- name: --json
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type: boolean_true
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description: |
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Write report in JSON format to this file.
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- name: --output
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type: file
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description: |
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Glob pattern for matching the expected output files.
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Should include `$output_dir`.
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example: "fastq/*_001.fast[a,q]"
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direction: output
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required: true
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must_exist: true
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multiple: true
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- name: --fasta
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type: boolean_true
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description: |
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Output FASTA to standard output even on FASTQ input.
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- name: --info_file
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type: boolean_true
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description: |
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Write information about each read and its adapter matches
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into info.txt in the output directory.
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See the documentation for the file format.
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# - name: -Z
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# - name: --rest_file
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# - name: --wildcard-file
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# - name: --too_short_output
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# - name: --too_long_output
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# - name: --untrimmed_output
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# - name: --untrimmed_paired_output
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# - name: too_short_paired_output
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# - name: too_long_paired_output
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- name: Debug
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arguments:
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- type: boolean_true
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name: --debug
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description: Print debug information
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resources:
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- type: bash_script
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path: script.sh
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test_resources:
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- type: bash_script
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path: test.sh
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engines:
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- type: docker
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image: python:3.12
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setup:
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- type: python
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pip:
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- cutadapt
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- type: docker
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run: |
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cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions.txt
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runners:
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- type: executable
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- type: nextflow
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