Commit ebade9a

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add fasta as parameter, move cager modules to nf-core style

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bin
conf
- modules.config
- test.config
modules/local/cager
- processing
  - environment.yml
  - main.nf
  - meta.yml
  - templates
    - cager_processing.R
  - tests
    - main.nf.test
    - nextflow.config
- readin
  - environment.yml
  - main.nf
  - meta.yml
  - templates
    - cager_readin.R
  - tests
- report
  - environment.yml
  - main.nf
  - meta.yml
  - templates
    - cager_report.R
  - tests
    - fixtures
      - dummy.Rmd
      - dummy.rds
    - main.nf.test
    - nextflow.config
- tag_qc
  - environment.yml
  - main.nf
  - meta.yml
  - templates
    - cager_tag_qc.R
  - tests
    - fixtures
      - dummy.rds
      - dummy.sqlite
    - main.nf.test
    - nextflow.config
- tagcluster_qc
  - environment.yml
  - main.nf
  - meta.yml
  - templates
    - cager_tagcluster_qc.R
  - tests
    - fixtures
      - dummy.rds
      - dummy.sqlite
    - main.nf.test
    - nextflow.config
nextflow.config
nextflow_schema.json
subworkflows/local
- prepare_mapping_metadata
  - main.nf
- utils_nfcore_cageseq_pipeline
  - main.nf
workflows
- cageseq.nf

`‎bin/cager_processing.R‎`

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