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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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Update 01-getting-started-with-nextflow.md with correct input fq.gz path #110

Closed emmcauley closed 6 months ago

emmcauley commented 6 months ago

Input fq.gz path given in "Your First Script" was params.input = "data/untrimmed_fastq/SRR2584863_1.fastq.gz instead of data/yeast/reads/ref1_1.fq.gz, which is the path given in the solution.

A straight-up copy + paste of the script produced the following output for me:

N E X T F L O W  ~  version 23.10.1
Launching `word_count.nf` [loving_chandrasekhar] DSL2 - revision: 72656509cb
executor >  local (1)
[60/c575b8] process > NUM_LINES (1) [100%] 1 of 1 ✔
SRR2584863_1.fastq.gz   0

which could be changed by overriding the params.input argument (nextflow run word_count.nf --input data/yeast/ref1_1.fq.gz:

N E X T F L O W  ~  version 23.10.1
Launching `word_count.nf` [friendly_dubinsky] DSL2 - revision: 72656509cb
executor >  local (1)
[aa/a655c0] process > NUM_LINES (1) [100%] 1 of 1 ✔
ref1_1.fq.gz    58708

This new output matches the solution given under Running Nextflow scripts > Show me the solution

github-actions[bot] commented 6 months ago

Thank you!

Thank you for your pull request :smiley:

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Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/workflows-nextflow/compare/md-outputs..md-outputs-PR-110

The following changes were observed in the rendered markdown documents:

 01-getting-started-with-nextflow.md | 2 +-
 02-workflow_parameters.md           | 2 +-
 md5sum.txt                          | 4 ++--
 3 files changed, 4 insertions(+), 4 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 2024-03-28 11:40:11 +0000