Deprecate checkmax/max_params docs #2739
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ewels
reviewed
Sep 25, 2024
| @@ -40,7 +40,7 @@ | |||
| /docs/usage/offline https://nf-core-docs.netlify.app/docs/usage/getting_started/offline 200 | |||
| /docs/usage/troubleshooting https://nf-core-docs.netlify.app/docs/usage/troubleshooting/overview 200 | |||
| /docs/usage/tutorials https://nf-core-docs.netlify.app/docs/tutorials 200 | |||
| /docs/usage/tutorials/step_by_step_institutional_profile https://nf-core-docs.netlify.app/docs/tutorials/use_nf-core_pipelines/config_institutional_profile 200 | |||
| /docs/usage/tutorials/step_by_step_institutional_profile https://nf-core-docs.netlify.app/docs/tutorials/use_nf-core_pipelines/writing_institutional_profile 200 | |||
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Should also add a new redirection rule as well if we are removing /config_institutional_profile
mirpedrol
reviewed
Sep 25, 2024
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| custom_config_version = 'master' | ||
| custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" |
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I would write the params scope or write it as params.custom_config_version to make it clear
Suggested change
| custom_config_version = 'master' | |
| custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" | |
| params { | |
| custom_config_version = 'master' | |
| custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" | |
| } |
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| For a more sophisticated `base.config`, see the full [nf-core template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config) | ||
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| 2. In a top level `nextflow.config`, specify two `param` to specify the URL where to look for nf-core/configs from. |
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Suggested change
| 2. In a top level `nextflow.config`, specify two `param` to specify the URL where to look for nf-core/configs from. | |
| 2. In a top level `nextflow.config`, specify two `params` to specify the URL where to look for nf-core/configs from. |
| } | ||
| ``` | ||
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| And supply this in your pipeline run command with `-c <custom>.conf`. Then, during a pipeline run, if for example a job exceeds the default memory request, it will be retried increasing the memory each time until either the job completes, or until it reaches a request of `256.GB`. |
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Suggested change
| And supply this in your pipeline run command with `-c <custom>.conf`. Then, during a pipeline run, if for example a job exceeds the default memory request, it will be retried increasing the memory each time until either the job completes, or until it reaches a request of `256.GB`. | |
| And supply this in your pipeline run command with `-c <custom>.config`. Then, during a pipeline run, if for example a job exceeds the default memory request, it will be retried increasing the memory each time until either the job completes, or until it reaches a request of `256.GB`. |
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It would be great someone can do a double check we've not left anything in.
We should also think about when this PR should be merged in... is it OK to do this now or should we sync with the tools update/release?