Update docs

[FriederikeHanssen]

#504

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[FriederikeHanssen]

I am more or less content with the restructuring/rewritting/overhauling of the section for "Input Smaplesheets", if anyone wants give some feedback on the current state @maxulysse @nickhsmith, pretty much anyone who will need to use this in the future.

[nickhsmith]

It looks good to me. I just think automatic input detection is a great feature, but it is at odds with the mandatory params input. That's my understanding of it.

[FriederikeHanssen]

We are planning on having this. Do you think this descirbes it well enough?:

The `Sarek`-generated `CSV` file is stored under `results/Preprocessing/CSV/duplicates_marked_no_table.csv` and will automatically be used as an input when specifying the parameter `--step prepare_recalibration`.

so rather maybe having a separate section on automatic restart?

[nickhsmith]

I think I'm confused on what we are discussing. This is for the documentation on how to use the different entry points correct? But The requirement of line 57 of main.nf which calls WorkflowMain.initialise(workflow, params, log) which requires:

if (!params.input) {                                                                                            
     log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"              
     System.exit(1)                                                                                              
 }

no matter what the params.input must be provided or it will not start the pipeline

is unaddressed. If the user provides params.input = 'recalibrated.csv' params.step = 'prepare_recalibration' (or whatever) that's a different behavior than just params.step = 'prepare_recalibration'

[FriederikeHanssen]

Yes, nothing is fixed here, it is just about the update to the usage.md and in there about the input samplesheets section: https://github.com/nf-core/sarek/blob/486aec71fbf0426f6b2eab54b52679a6fc54836f/docs/usage.md

The code fixes will be done in a separate PR

[nickhsmith]

Ok now I understand a bit more thanks for the added info! I think it's clear :)

[FriederikeHanssen]

ok, sorry I could have added more info. I was in the zone and I knew what I meant :D

[maxulysse]

why is there changes in workflows/sarek.nf?

[maxulysse]

It seems there's some conflicts as well

[FriederikeHanssen]

why is there changes in workflows/sarek.nf?

🤔 I'll rebase and see what happens. Just finishing up quickly the other PR

[FriederikeHanssen]

ok still irritated about the workflow changes. I think I'll just manually change them to what is in dev at the moment.