name: kallisto_index
namespace: kallisto
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/nf-core/kallisto/index/main.nf, modules/nf-core/kallisto/index/meta.yml]
    last_sha: c0816976384d5e7ee6079c29c45958df1ffa0ee4
description: | 
  Create Kallisto index.

argument_groups:
- name: "Input"
  arguments: 
  - name: "--transcriptome_fasta"
    type: file
  - name: "--pseudo_aligner_kmer_size"
    type: integer
    description: Kmer length passed to indexing step of pseudoaligners.

- name: "Output"
  arguments:
  - name: "--kallisto_index"
    type: file
    direction: output
    default: Kallisto_index

resources:
  - type: bash_script
    path: script.sh

test_resources:
  - type: bash_script
    path: test.sh
  - path: /testData/minimal_test/reference/transcriptome.fasta

engines:
  - type: docker
    image: ubuntu:22.04
    setup:
      - type: docker
        run: |
          apt-get update && \
          apt-get install -y --no-install-recommends wget && \
          wget --no-check-certificate https://github.com/pachterlab/kallisto/releases/download/v0.50.1/kallisto_linux-v0.50.1.tar.gz && \
          tar -xzf kallisto_linux-v0.50.1.tar.gz && \
          mv kallisto/kallisto /usr/local/bin/
runners:
  - type: executable
  - type: nextflow