nf-core / nf-core/nascent

Sample names must contain at least underscore (?)

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bug
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Description

Description of the bug

Hey!

I was running the nascent pipeline v2.1.1 (v2.2.0 didn't work due to #) for two runs of the same sample.

I encountered an error at the step of samtools sort:

[51/e45e94] Submitted process > NFCORE_NASCENT:NASCENT:ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (EXP_T1)
Pulling Singularity image https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0 [cache /resources/containers/depot.galaxyproject.org-singularity-mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690-e8a286b2e789c091bac0a57302cdc78aa0112353-0.img]
ERROR ~ fromIndex = -1

 -- Check script '/users/dmitry.mylarshchikov/.nextflow/assets/nf-core/nascent/./workflows/nascent.nf' at line: 222 or see '.nextflow.log' file for more details
[5a/85327c] Submitted process > NFCORE_NASCENT:NASCENT:ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (EXP_T1)

I checked out #113, but solution was not applicable to my case. By trying different things, I found out that the reason is in the sample name. Initially, I put a name EXP, and it failed. I put a longer name, DUTTKE and it failed again. But it is running now fine with sample name DUTTKE_REP1.

So, apparently, v2.1.1 requires sample names to have at least one underscore. I cannot test it on v2.2.0 due to another bug, but could you please add this info to the docs?

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System information

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Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by checking the current documentation for sample-name requirements and compare it with the behavior described for v2.1.1. The report points to workflows/nascent.nf line 222 and .nextflow.log for the failure; done means documenting the confirmed requirement, including the affected version and a working example such as DUTTKE_REP1.

Written by the indexing model from the issue text.

Assessment

Domain
documentation
Issue type
Documentation
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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