CI
c7c4845b30
Build pipeline: viash-hub.htrnaseq.v0.5-nr288
Source commit: 04bc53879d
Source message: Bump version to v0.5.5
81 lines
2.0 KiB
YAML
81 lines
2.0 KiB
YAML
name: runner
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namespace: workflows
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description: Runner for HT RNA-seq pipeline
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argument_groups:
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- name: Input arguments
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arguments:
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- name: --input
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description: Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`
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multiple: true
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type: file
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required: true
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- name: --barcodesFasta
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type: file
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required: true
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- name: --genomeDir
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type: file
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required: true
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- name: --annotation
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type: file
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required: true
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- name: --ignore
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description: "Pool names to ignore."
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type: string
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multiple: true
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default: ["Undetermined"]
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- name: "--umi_length"
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description: |
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Length of the UMI sequences
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type: integer
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min: 1
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default: 10
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- name: Metadata arguments
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arguments:
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- name: --id
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description: Unique identifier for the run
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type: string
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- name: --project_id
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description: Project ID
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type: string
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required: true
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- name: --experiment_id
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description: Experiment ID
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type: string
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required: true
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- name: Annotation flags
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arguments:
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- name: --plain_output
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description: |
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Flag to indicate that the output should be stored directly under $publish_dir rather than
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under a subdirectory structure runID/<date_time>_demultiplex_<version>/.
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type: boolean_true
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- name: Publish arguments
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arguments:
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- name: --fastq_publish_dir
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type: string
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required: true
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- name: --results_publish_dir
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type: string
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required: true
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resources:
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- type: nextflow_script
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path: main.nf
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entrypoint: run_wf
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dependencies:
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- name: utils/listInputDir
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repository: local
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- name: workflows/htrnaseq
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repository: local
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- name: io/publish_fastqs
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repository: local
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- name: io/publish_results
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repository: local
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runners:
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- type: nextflow
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engines:
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- type: native
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