Arriba¶
Arriba
· 1 contributor · 2 versions
Arriba gene fusion detector¶
Version: 1.2.0 Arriba is a fast tool to search for aberrant transcripts such as gene fusions. It is based on chimeric alignments found by the STAR RNA-Seq aligner.
Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. It is based on the ultrafast STAR aligner and the post-alignment runtime is typically just ~2 minutes. In contrast to many other fusion detection tools which build on STAR, Arriba does not require to reduce the alignIntronMax parameter of STAR to detect fusions arising from focal deletions.
Apart from gene fusions, Arriba can detect other structural rearrangements with potential clinical relevance, such as exon duplications or truncations of genes (i.e., breakpoints in introns and intergenic regions).
Quickstart¶
from janis_bioinformatics.tools.suhrig.arriba.versions import Arriba_1_2_0 wf = WorkflowBuilder("myworkflow") wf.step( "arriba_step", Arriba_1_2_0( aligned_inp=None, ) ) wf.output("out", source=arriba_step.out) wf.output("out_discarded", source=arriba_step.out_discarded)
OR
- Install Janis
- Ensure Janis is configured to work with Docker or Singularity.
- Ensure all reference files are available:
Note
More information about these inputs are available below.
- Generate user input files for Arriba:
# user inputs
janis inputs Arriba > inputs.yaml
inputs.yaml
aligned_inp: aligned_inp.bam
- Run Arriba with:
janis run [...run options] \
--inputs inputs.yaml \
Arriba
Information¶
ID: | Arriba |
---|---|
URL: | No URL to the documentation was provided |
Versions: | 1.2.0, 1.1.0 |
Container: | quay.io/biocontainers/arriba:1.2.0–hd2e4403_2 |
Authors: | Michael Franklin |
Citations: | None |
Created: | 2020-09-02 |
Updated: | 2020-09-02 |
Outputs¶
name | type | documentation |
---|---|---|
out | tsv | |
out_discarded | tsv |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
aligned_inp | BAM | -x | File in SAM/BAM/CRAM format with main alignments as generated by STAR (Aligned.out.sam). Arriba extracts candidate reads from this file. This is sometimes /dev/stdin | |
inp_chimeric | Optional<BAM> | -c | File in SAM/BAM/CRAM format with chimeric alignments as generated by STAR (Chimeric.out.sam). This parameter is only required, if STAR was run with the parameter ‘–chimOutType SeparateSAMold’. When STAR was run with the parameter ‘–chimOutType WithinBAM’, it suffices to pass the parameter -x to Arriba and -c can be omitted. | |
gtf_file | Optional<File> | -g | GTF file with gene annotation. The file may be gzip-compressed. | |
gtf_features | Optional<csv> | -G | Comma-/space-separated list of names of GTF features. Default: gene_name=gene_name|gene_id gene_id=gene_id transcript_id=transcript_id feature_exon=exon feature_CDS=CDS | |
reference | Optional<Fasta> | -a | FastA file with genome sequence (assembly). The file may be gzip-compressed. An index with the file extension .fai must exist only if CRAM files are processed. | |
blacklist | Optional<File> | -b | File containing blacklisted events (recurrent artifacts and transcripts observed in healthy tissue). | |
known_fusions | Optional<tsv> | -k | File containing known/recurrent fusions. Some cancer entities are often characterized by fusions between the same pair of genes. In order to boost sensitivity, a list of known fusions can be supplied using this parameter. The list must contain two columns with the names of the fused genes, separated by tabs. | |
output_filename | Optional<Filename> | -o | Output file with fusions that have passed all filters. | |
discarded_output_filename | Optional<Filename> | -O | Output file with fusions that were discarded due to filtering. | |
structural_variants_coordinates | Optional<tsv> | -d | Tab-separated file with coordinates of structural variants found using whole-genome sequencing data. These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence. | |
max_genomic_breakpoint_distance | Optional<Integer> | -D | When a file with genomic breakpoints obtained via whole-genome sequencing is supplied via the -d parameter, this parameter determines how far a genomic breakpoint may be away from a transcriptomic breakpoint to consider it as a related event. For events inside genes, the distance is added to the end of the gene; for intergenic events, the distance threshold is applied as is. Default: 100000 | |
strandedness | Optional<String> | -s | Whether a strand-specific protocol was used for library preparation, and if so, the type of strandedness (auto/yes/no/reverse). When unstranded data is processed, the strand can sometimes be inferred from splice-patterns. But in unclear situations, stranded data helps resolve ambiguities. Default: auto | |
contigs | Optional<Array<String>> | -i | Comma-/space-separated list of interesting contigs. Fusions between genes on other contigs are ignored. Contigs can be specified with or without the prefix ‘chr’. Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y | |
filters | Optional<Array<String>> | -f | Comma-/space-separated list of filters to disable. By default all filters are enabled. Valid values: homopolymer, same_gene, inconsistently_clipped, duplicates, low_entropy, no_genomic_support, short_anchor, homologs, blacklist, pcr_fusions, isoforms, intronic, uninteresting_contigs, read_through, genomic_support, mismatches, no_coverage, spliced, mismappers, merge_adjacent, select_best, many_spliced, long_gap, min_support, relative_support, end_to_end, known_fusions, non_coding_neighbors, intragenic_exonic, hairpin, small_insert_size | |
max_e_value | Optional<Float> | -E | Arriba estimates the number of fusions with a given number of supporting reads which one would expect to see by random chance. If the expected number of fusions (e-value) is higher than this threshold, the fusion is discarded by the ‘relative_support’ filter. Note: Increasing this threshold can dramatically increase the number of false positives and may increase the runtime of resource-intensive steps. Fractional values are possible. Default: 0.300000 | |
min_supporting_reads | Optional<Integer> | -S | The ‘min_support’ filter discards all fusions with fewer than this many supporting reads (split reads and discordant mates combined). Default: 2 | |
max_mismappers | Optional<Float> | -m | When more than this fraction of supporting reads turns out to be mismappers, the ‘mismappers’ filter discards the fusion. Default: 0.800000 | |
max_homolog_identity | Optional<Float> | -L | Genes with more than the given fraction of sequence identity are considered homologs and removed by the ‘homologs’ filter. Default: 0.300000 | |
homopolymer_length | Optional<Integer> | -H | The ‘homopolymer’ filter removes breakpoints adjacent to homopolymers of the given length or more. Default: 6 | |
read_through_distance | Optional<Integer> | -R | The ‘read_through’ filter removes read-through fusions where the breakpoints are less than the given distance away from each other. Default: 10000 | |
min_anchor_length | Optional<Integer> | -A | Alignment artifacts are often characterized by split reads coming from only one gene and no discordant mates. Moreover, the split reads only align to a short stretch in one of the genes. The ‘short_anchor’ filter removes these fusions. This parameter sets the threshold in bp for what the filter considers short. Default: 23 | |
many_spliced_events | Optional<Integer> | -M | The ‘many_spliced’ filter recovers fusions between genes that have at least this many spliced breakpoints. Default: 4 | |
max_kmer_content | Optional<Float> | -K | The ‘low_entropy’ filter removes reads with repetitive 3-mers. If the 3-mers make up more than the given fraction of the sequence, then the read is discarded. Default: 0.600000 | |
max_mismatch_pvalue | Optional<Float> | -V | The ‘mismatches’ filter uses a binomial model to calculate a p-value for observing a given number of mismatches in a read. If the number of mismatches is too high, the read is discarded. Default: 0.010000 | |
fragment_length | Optional<Integer> | -F | When paired-end data is given, the fragment length is estimated automatically and this parameter has no effect. But when single-end data is given, the mean fragment length should be specified to effectively filter fusions that arise from hairpin structures. Default: 200 | |
max_reads | Optional<Integer> | -U | Subsample fusions with more than the given number of supporting reads. This improves performance without compromising sensitivity, as long as the threshold is high. Counting of supporting reads beyond the threshold is inaccurate, obviously. Default: 300 | |
quantile | Optional<Float> | -Q | Highly expressed genes are prone to produce artifacts during library preparation. Genes with an expression above the given quantile are eligible for filtering by the ‘pcr_fusions’ filter. Default: 0.998000 | |
exonic_fraction | Optional<Float> | -e | The breakpoints of false-positive predictions of intragenic events are often both in exons. True predictions are more likely to have at least one breakpoint in an intron, because introns are larger. If the fraction of exonic sequence between two breakpoints is smaller than the given fraction, the ‘intragenic_exonic’ filter discards the event. Default: 0.200000 | |
fusion_transcript | Optional<Boolean> | -T | When set, the column ‘fusion_transcript’ is populated with the sequence of the fused genes as assembled from the supporting reads. Specify the flag twice to also print the fusion transcripts to the file containing discarded fusions (-O). Default: off | |
peptide_sequence | Optional<Boolean> | -P | When set, the column ‘peptide_sequence’ is populated with the sequence of the fused proteins as assembled from the supporting reads. Specify the flag twice to also print the peptide sequence to the file containing discarded fusions (-O). Default: off | |
read_identifiers | Optional<Boolean> | -I | When set, the column ‘read_identifiers’ is populated with identifiers of the reads which support the fusion. The identifiers are separated by commas. Specify the flag twice to also print the read identifiers to the file containing discarded fusions (-O). Default: off |
Workflow Description Language¶
version development
task Arriba {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
File aligned_inp
File? inp_chimeric
File? gtf_file
File? gtf_features
File? reference
File? blacklist
File? known_fusions
String? output_filename
String? discarded_output_filename
File? structural_variants_coordinates
Int? max_genomic_breakpoint_distance
String? strandedness
Array[String]? contigs
Array[String]? filters
Float? max_e_value
Int? min_supporting_reads
Float? max_mismappers
Float? max_homolog_identity
Int? homopolymer_length
Int? read_through_distance
Int? min_anchor_length
Int? many_spliced_events
Float? max_kmer_content
Float? max_mismatch_pvalue
Int? fragment_length
Int? max_reads
Float? quantile
Float? exonic_fraction
Boolean? fusion_transcript
Boolean? peptide_sequence
Boolean? read_identifiers
}
command <<<
set -e
arriba \
-x '~{aligned_inp}' \
~{if defined(inp_chimeric) then ("-c '" + inp_chimeric + "'") else ""} \
~{if defined(gtf_file) then ("-g '" + gtf_file + "'") else ""} \
~{if defined(gtf_features) then ("-G '" + gtf_features + "'") else ""} \
~{if defined(reference) then ("-a '" + reference + "'") else ""} \
~{if defined(blacklist) then ("-b '" + blacklist + "'") else ""} \
~{if defined(known_fusions) then ("-k '" + known_fusions + "'") else ""} \
-o '~{select_first([output_filename, "generated.tsv"])}' \
-O '~{select_first([discarded_output_filename, "generated.discarded.tsv"])}' \
~{if defined(structural_variants_coordinates) then ("-d '" + structural_variants_coordinates + "'") else ""} \
~{if defined(max_genomic_breakpoint_distance) then ("-D " + max_genomic_breakpoint_distance) else ''} \
~{if defined(strandedness) then ("-s '" + strandedness + "'") else ""} \
~{if (defined(contigs) && length(select_first([contigs])) > 0) then "-i '" + sep("' '", select_first([contigs])) + "'" else ""} \
~{if (defined(filters) && length(select_first([filters])) > 0) then "-f '" + sep("' '", select_first([filters])) + "'" else ""} \
~{if defined(max_e_value) then ("-E " + max_e_value) else ''} \
~{if defined(min_supporting_reads) then ("-S " + min_supporting_reads) else ''} \
~{if defined(max_mismappers) then ("-m " + max_mismappers) else ''} \
~{if defined(max_homolog_identity) then ("-L " + max_homolog_identity) else ''} \
~{if defined(homopolymer_length) then ("-H " + homopolymer_length) else ''} \
~{if defined(read_through_distance) then ("-R " + read_through_distance) else ''} \
~{if defined(min_anchor_length) then ("-A " + min_anchor_length) else ''} \
~{if defined(many_spliced_events) then ("-M " + many_spliced_events) else ''} \
~{if defined(max_kmer_content) then ("-K " + max_kmer_content) else ''} \
~{if defined(max_mismatch_pvalue) then ("-V " + max_mismatch_pvalue) else ''} \
~{if defined(fragment_length) then ("-F " + fragment_length) else ''} \
~{if defined(max_reads) then ("-U " + max_reads) else ''} \
~{if defined(quantile) then ("-Q " + quantile) else ''} \
~{if defined(exonic_fraction) then ("-e " + exonic_fraction) else ''} \
~{if (defined(fusion_transcript) && select_first([fusion_transcript])) then "-T" else ""} \
~{if (defined(peptide_sequence) && select_first([peptide_sequence])) then "-P" else ""} \
~{if (defined(read_identifiers) && select_first([read_identifiers])) then "-I" else ""}
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "quay.io/biocontainers/arriba:1.2.0--hd2e4403_2"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 4])}G"
preemptible: 2
}
output {
File out = select_first([output_filename, "generated.tsv"])
File out_discarded = select_first([discarded_output_filename, "generated.discarded.tsv"])
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Arriba
doc: |2
Arriba gene fusion detector
---------------------------
Version: 1.2.0
Arriba is a fast tool to search for aberrant transcripts such as gene fusions.
It is based on chimeric alignments found by the STAR RNA-Seq aligner.
Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a
clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. It is based
on the ultrafast STAR aligner and the post-alignment runtime is typically just ~2 minutes. In contrast to many other
fusion detection tools which build on STAR, Arriba does not require to reduce the alignIntronMax parameter of STAR
to detect fusions arising from focal deletions.
Apart from gene fusions, Arriba can detect other structural rearrangements with potential clinical relevance, such
as exon duplications or truncations of genes (i.e., breakpoints in introns and intergenic regions).
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: quay.io/biocontainers/arriba:1.2.0--hd2e4403_2
inputs:
- id: aligned_inp
label: aligned_inp
doc: |-
File in SAM/BAM/CRAM format with main alignments as generated by STAR (Aligned.out.sam). Arriba extracts candidate reads from this file. This is sometimes /dev/stdin
type: File
inputBinding:
prefix: -x
separate: true
- id: inp_chimeric
label: inp_chimeric
doc: |-
File in SAM/BAM/CRAM format with chimeric alignments as generated by STAR (Chimeric.out.sam). This parameter is only required, if STAR was run with the parameter '--chimOutType SeparateSAMold'. When STAR was run with the parameter '--chimOutType WithinBAM', it suffices to pass the parameter -x to Arriba and -c can be omitted.
type:
- File
- 'null'
inputBinding:
prefix: -c
separate: true
- id: gtf_file
label: gtf_file
doc: GTF file with gene annotation. The file may be gzip-compressed.
type:
- File
- 'null'
inputBinding:
prefix: -g
separate: true
- id: gtf_features
label: gtf_features
doc: |-
Comma-/space-separated list of names of GTF features. Default: gene_name=gene_name|gene_id gene_id=gene_id transcript_id=transcript_id feature_exon=exon feature_CDS=CDS
type:
- File
- 'null'
inputBinding:
prefix: -G
separate: true
- id: reference
label: reference
doc: |-
FastA file with genome sequence (assembly). The file may be gzip-compressed. An index with the file extension .fai must exist only if CRAM files are processed.
type:
- File
- 'null'
inputBinding:
prefix: -a
separate: true
- id: blacklist
label: blacklist
doc: |-
File containing blacklisted events (recurrent artifacts and transcripts observed in healthy tissue).
type:
- File
- 'null'
inputBinding:
prefix: -b
separate: true
- id: known_fusions
label: known_fusions
doc: |-
File containing known/recurrent fusions. Some cancer entities are often characterized by fusions between the same pair of genes. In order to boost sensitivity, a list of known fusions can be supplied using this parameter. The list must contain two columns with the names of the fused genes, separated by tabs.
type:
- File
- 'null'
inputBinding:
prefix: -k
separate: true
- id: output_filename
label: output_filename
doc: Output file with fusions that have passed all filters.
type:
- string
- 'null'
default: generated.tsv
inputBinding:
prefix: -o
separate: true
- id: discarded_output_filename
label: discarded_output_filename
doc: Output file with fusions that were discarded due to filtering.
type:
- string
- 'null'
default: generated.discarded.tsv
inputBinding:
prefix: -O
separate: true
- id: structural_variants_coordinates
label: structural_variants_coordinates
doc: |-
Tab-separated file with coordinates of structural variants found using whole-genome sequencing data. These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence.
type:
- File
- 'null'
inputBinding:
prefix: -d
separate: true
- id: max_genomic_breakpoint_distance
label: max_genomic_breakpoint_distance
doc: |-
When a file with genomic breakpoints obtained via whole-genome sequencing is supplied via the -d parameter, this parameter determines how far a genomic breakpoint may be away from a transcriptomic breakpoint to consider it as a related event. For events inside genes, the distance is added to the end of the gene; for intergenic events, the distance threshold is applied as is. Default: 100000
type:
- int
- 'null'
inputBinding:
prefix: -D
separate: true
- id: strandedness
label: strandedness
doc: |-
Whether a strand-specific protocol was used for library preparation, and if so, the type of strandedness (auto/yes/no/reverse). When unstranded data is processed, the strand can sometimes be inferred from splice-patterns. But in unclear situations, stranded data helps resolve ambiguities. Default: auto
type:
- string
- 'null'
inputBinding:
prefix: -s
separate: true
- id: contigs
label: contigs
doc: |-
Comma-/space-separated list of interesting contigs. Fusions between genes on other contigs are ignored. Contigs can be specified with or without the prefix 'chr'. Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y
type:
- type: array
items: string
- 'null'
inputBinding:
prefix: -i
- id: filters
label: filters
doc: |-
Comma-/space-separated list of filters to disable. By default all filters are enabled. Valid values: homopolymer, same_gene, inconsistently_clipped, duplicates, low_entropy, no_genomic_support, short_anchor, homologs, blacklist, pcr_fusions, isoforms, intronic, uninteresting_contigs, read_through, genomic_support, mismatches, no_coverage, spliced, mismappers, merge_adjacent, select_best, many_spliced, long_gap, min_support, relative_support, end_to_end, known_fusions, non_coding_neighbors, intragenic_exonic, hairpin, small_insert_size
type:
- type: array
items: string
- 'null'
inputBinding:
prefix: -f
itemSeparator: ' '
- id: max_e_value
label: max_e_value
doc: |-
Arriba estimates the number of fusions with a given number of supporting reads which one would expect to see by random chance. If the expected number of fusions (e-value) is higher than this threshold, the fusion is discarded by the 'relative_support' filter. Note: Increasing this threshold can dramatically increase the number of false positives and may increase the runtime of resource-intensive steps. Fractional values are possible. Default: 0.300000
type:
- float
- 'null'
inputBinding:
prefix: -E
separate: true
- id: min_supporting_reads
label: min_supporting_reads
doc: |-
The 'min_support' filter discards all fusions with fewer than this many supporting reads (split reads and discordant mates combined). Default: 2
type:
- int
- 'null'
inputBinding:
prefix: -S
separate: true
- id: max_mismappers
label: max_mismappers
doc: |-
When more than this fraction of supporting reads turns out to be mismappers, the 'mismappers' filter discards the fusion. Default: 0.800000
type:
- float
- 'null'
inputBinding:
prefix: -m
separate: true
- id: max_homolog_identity
label: max_homolog_identity
doc: |-
Genes with more than the given fraction of sequence identity are considered homologs and removed by the 'homologs' filter. Default: 0.300000
type:
- float
- 'null'
inputBinding:
prefix: -L
separate: true
- id: homopolymer_length
label: homopolymer_length
doc: |-
The 'homopolymer' filter removes breakpoints adjacent to homopolymers of the given length or more. Default: 6
type:
- int
- 'null'
inputBinding:
prefix: -H
separate: true
- id: read_through_distance
label: read_through_distance
doc: |-
The 'read_through' filter removes read-through fusions where the breakpoints are less than the given distance away from each other. Default: 10000
type:
- int
- 'null'
inputBinding:
prefix: -R
separate: true
- id: min_anchor_length
label: min_anchor_length
doc: |-
Alignment artifacts are often characterized by split reads coming from only one gene and no discordant mates. Moreover, the split reads only align to a short stretch in one of the genes. The 'short_anchor' filter removes these fusions. This parameter sets the threshold in bp for what the filter considers short. Default: 23
type:
- int
- 'null'
inputBinding:
prefix: -A
separate: true
- id: many_spliced_events
label: many_spliced_events
doc: |-
The 'many_spliced' filter recovers fusions between genes that have at least this many spliced breakpoints. Default: 4
type:
- int
- 'null'
inputBinding:
prefix: -M
separate: true
- id: max_kmer_content
label: max_kmer_content
doc: |-
The 'low_entropy' filter removes reads with repetitive 3-mers. If the 3-mers make up more than the given fraction of the sequence, then the read is discarded. Default: 0.600000
type:
- float
- 'null'
inputBinding:
prefix: -K
separate: true
- id: max_mismatch_pvalue
label: max_mismatch_pvalue
doc: |-
The 'mismatches' filter uses a binomial model to calculate a p-value for observing a given number of mismatches in a read. If the number of mismatches is too high, the read is discarded. Default: 0.010000
type:
- float
- 'null'
inputBinding:
prefix: -V
separate: true
- id: fragment_length
label: fragment_length
doc: |-
When paired-end data is given, the fragment length is estimated automatically and this parameter has no effect. But when single-end data is given, the mean fragment length should be specified to effectively filter fusions that arise from hairpin structures. Default: 200
type:
- int
- 'null'
inputBinding:
prefix: -F
separate: true
- id: max_reads
label: max_reads
doc: |-
Subsample fusions with more than the given number of supporting reads. This improves performance without compromising sensitivity, as long as the threshold is high. Counting of supporting reads beyond the threshold is inaccurate, obviously. Default: 300
type:
- int
- 'null'
inputBinding:
prefix: -U
separate: true
- id: quantile
label: quantile
doc: |-
Highly expressed genes are prone to produce artifacts during library preparation. Genes with an expression above the given quantile are eligible for filtering by the 'pcr_fusions' filter. Default: 0.998000
type:
- float
- 'null'
inputBinding:
prefix: -Q
separate: true
- id: exonic_fraction
label: exonic_fraction
doc: |-
The breakpoints of false-positive predictions of intragenic events are often both in exons. True predictions are more likely to have at least one breakpoint in an intron, because introns are larger. If the fraction of exonic sequence between two breakpoints is smaller than the given fraction, the 'intragenic_exonic' filter discards the event. Default: 0.200000
type:
- float
- 'null'
inputBinding:
prefix: -e
separate: true
- id: fusion_transcript
label: fusion_transcript
doc: |-
When set, the column 'fusion_transcript' is populated with the sequence of the fused genes as assembled from the supporting reads. Specify the flag twice to also print the fusion transcripts to the file containing discarded fusions (-O). Default: off
type:
- boolean
- 'null'
inputBinding:
prefix: -T
separate: true
- id: peptide_sequence
label: peptide_sequence
doc: |-
When set, the column 'peptide_sequence' is populated with the sequence of the fused proteins as assembled from the supporting reads. Specify the flag twice to also print the peptide sequence to the file containing discarded fusions (-O). Default: off
type:
- boolean
- 'null'
inputBinding:
prefix: -P
separate: true
- id: read_identifiers
label: read_identifiers
doc: |-
When set, the column 'read_identifiers' is populated with identifiers of the reads which support the fusion. The identifiers are separated by commas. Specify the flag twice to also print the read identifiers to the file containing discarded fusions (-O). Default: off
type:
- boolean
- 'null'
inputBinding:
prefix: -I
separate: true
outputs:
- id: out
label: out
type: File
outputBinding:
glob: generated.tsv
loadContents: false
- id: out_discarded
label: out_discarded
type: File
outputBinding:
glob: generated.discarded.tsv
loadContents: false
stdout: _stdout
stderr: _stderr
baseCommand:
- arriba
arguments: []
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: Arriba