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DESeq2 fails with only one sample #649

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c-mertes opened this issue Jun 3, 2021 · 1 comment
Closed
2 tasks done

DESeq2 fails with only one sample #649

c-mertes opened this issue Jun 3, 2021 · 1 comment
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bug Something isn't working
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3.2

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@c-mertes
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c-mertes commented Jun 3, 2021

Running the full pipeline with just one sample will fail to run the DESeq2 QC part as DESeq2 needs at least two samples to estimate the dispersion.

One solution would be to ignore the QC by providing --skip_deseq2 but it would be nicer if it is checked within the pipeline and skipped automatically.

This is probably related to #641 and #635.

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I have checked the following places for your error:

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

  1. Create a sample sheet with just one sample
  2. run pipeline with defaults

Expected behaviour

To ignore the deseq2 qc step.
@c-mertes c-mertes added the bug Something isn't working label Jun 3, 2021
@drpatelh drpatelh added this to the 3.2 milestone Jun 15, 2021
drpatelh added a commit to drpatelh/nf-core-rnaseq that referenced this issue Jun 16, 2021
@drpatelh
Fix nf-core#649
1655437
@drpatelh drpatelh mentioned this issue Jun 16, 2021
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drpatelh commented Jun 16, 2021 •
edited

Will be fixed in #655.

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