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carpentries-incubator / workflows-nextflow

Workflow management with Nextflow and nf-core
https://carpentries-incubator.github.io/workflows-nextflow/
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18 stars 29 forks source link

Lesson cleanup #97

Closed ggrimes closed 7 months ago

github-actions[bot] commented 7 months ago

Thank you!

Thank you for your pull request :smiley:

:robot: This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/workflows-nextflow/compare/md-outputs..md-outputs-PR-97

The following changes were observed in the rendered markdown documents:

 01-getting-started-with-nextflow.md                |  95 +++-------------
 ...flow_parameters.md => 02-workflow_parameters.md |  28 ++---
 04-channels.md => 03-channels.md                   |  46 +++++++-
 05-processes-part1.md => 04-processes-part1.md     |  20 +++-
 12-reporting.md => 08-reporting.md                 |   0
 08-configuration.md => 09-configuration.md         |   0
 ...caching.md => 10-workflow_checkpoint_caching.md |   0
 ...eq_pipeline.md => 11-Simple_Rna-Seq_pipeline.md | 125 +++++++++++----------
 10-Modules.md => 12-Modules.md                     |   0
 11-subworkflows.md => 13-subworkflows.md           |   0
 ...xtflow_scripting.md => 16-nextflow_scripting.md |   0
 config.yaml                                        |  20 ++--
 .../channel_exercise_val-queue_answer.nf (new)     |   4 +
 files/scripts/introduction/word_count.nf (new)     |  59 ++++++++++
 files/scripts/parameters/word_count.nf (new)       |  51 +++++++++
 files/scripts/rnaseq_pipeline/script2.nf           |   2 +-
 md5sum.txt                                         |  26 ++---
 setup.md                                           |  82 +++++++++-----
 18 files changed, 343 insertions(+), 215 deletions(-)
What does this mean? If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

:stopwatch: Updated at 2023-12-11 16:42:02 +0000