nf-core_modules/tests/modules/sratools/prefetch/test.yml at 8f7e5c050ee99d277b4ed0c596962ee79fc769a8 - millironx/nf-core_modules - Milliron X Code: Code hosting for cattle or technology, but especially anything to do with both of them

millironx/nf-core_modules

mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-15 06:03:10 +00:00

Moritz E. Beber 07c0830057

Add a module for sra-tools prefetch (#714 )

* chore: apply module template

* refactor: add NCBI settings to options

* docs: complete meta information

* feat: add prefetch process

* fix: correct bash commands

* tests: define the right tests

* style: move option definition to satisfy linting

* fix: extract version correctly

* fix: correct newline issues

* refactor: address review comments

* Apply suggestions from code review

* chore: add retrying via nf-core label

* refactor: validate download thoroughly

* refactor: remove vdb-config input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

2021-10-11 22:30:41 +01:00

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 - name: sratools prefetch test_sratools_prefetch
   command: nextflow run tests/modules/sratools/prefetch -entry test_sratools_prefetch -c tests/config/nextflow.config
   tags:
     - sratools/prefetch
     - sratools
   files:
     - path: output/sratools/ERR2815334/ERR2815334.sra
       md5sum: 9a98c7f6f4774b7ef94aa915b92a54ea