name: "rsem_merge_counts"
namespace: "rsem"
info:
  migration_info:
    git_repo: https://github.com/nf-core/rnaseq.git
    paths: [modules/local/rsem_merge_counts/main.nf]
    last_sha: 311279532694ce7520164ce4d65a388c0cd11f60

description: | 
  Merge the transcript quantification results obtained from rsem calculate-expression across all samples.

argument_groups:
- name: "Input"
  arguments:
  - name: "--counts_gene"
    type: file
    description: Expression counts on gene level (genes)
  - name: "--counts_transcripts"
    type: file
    description: Expression counts on transcript level (isoforms)
  - name: "--versions"
    type: file
    must_exist: false

- name: "Output"
  arguments: 
  - name: "--merged_gene_counts"
    type: file
    description: File containing gene counts across all samples.
    default: rsem.merged.gene_counts.tsv
    direction: output
  - name: "--merged_gene_tpm"
    type: file
    description: File containing gene TPM across all samples.
    default: rsem.merged.gene_tpm.tsv
    direction: output
  - name: "--merged_transcript_counts"
    type: file
    description: File containing transcript counts across all samples.
    default: rsem.merged.transcript_counts.tsv
    direction: output
  - name: "--merged_transcript_tpm"
    type: file
    description: File containing transcript TPM across all samples.
    default: rsem.merged.transcript_tpm.tsv
    direction: output
  - name: "--updated_versions"
    type: file
    default: versions.yml
    direction: output

resources:
  - type: bash_script
    path: script.sh

# test_resources:
#   - type: bash_script
#     path: test.sh
  # - path: /testData/minimal_test/input_fastq/SRR6357070_1.fastq.gz
  # - path: /testData/minimal_test/input_fastq/SRR6357070_2.fastq.gz

engines:
  - type: docker
    image: ubuntu:22.04
    
runners:
  - type: executable
  - type: nextflow
