50 lines
1.3 KiB
YAML
50 lines
1.3 KiB
YAML
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name: kallisto_index
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namespace: kallisto
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info:
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migration_info:
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git_repo: https://github.com/nf-core/rnaseq.git
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paths: [modules/nf-core/kallisto/index/main.nf, modules/nf-core/kallisto/index/meta.yml]
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last_sha: c0816976384d5e7ee6079c29c45958df1ffa0ee4
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description: |
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Create Kallisto index.
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argument_groups:
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- name: "Input"
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arguments:
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- name: "--transcriptome_fasta"
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type: file
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- name: "--pseudo_aligner_kmer_size"
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type: integer
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description: Kmer length passed to indexing step of pseudoaligners.
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- name: "Output"
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arguments:
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- name: "--kallisto_index"
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type: file
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direction: output
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default: Kallisto_index
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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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- path: /testData/minimal_test/reference/transcriptome.fasta
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engines:
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- type: docker
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image: ubuntu:22.04
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setup:
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- type: docker
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run: |
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apt-get update && \
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apt-get install -y --no-install-recommends wget && \
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wget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz && \
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tar -xzf kallisto_linux-v0.50.1.tar.gz && \
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mv kallisto/kallisto /usr/local/bin/
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runners:
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- type: executable
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- type: nextflow
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