add Shifter + Charliecloud profiles #826
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## dev #826 +/- ##
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Coverage 77.77% 77.78%
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Files 22 22
Lines 2529 2530 +1
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+ Hits 1967 1968 +1
Misses 562 562
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indicates the necessity to add all required software to the path. This is important for pipelines with multiple environments.
as suggested by @ewels in nf-core#824 (comment)
ewels
approved these changes
Feb 3, 2021
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| env { | ||
| PATH = "/opt/conda/bin:/opt/conda/envs/{{ cookiecutter.name_noslash }}-{{ cookiecutter.version }}/bin:$PATH" | ||
| // TODO nf-core: If the pipeline uses additional environments, add them to $PATH as well |
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Any idea how this will work with BioContainers as used in DSL2 pipelines?
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Should work as the path will always be the same for Biocontainers, so the first /opt/conda/bin should cover this nicely 👍🏻
nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md
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…sage.md Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
apeltzer
approved these changes
Feb 5, 2021
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Closes #824