Allow generating contact maps for multiple samples

muffato commented 11 months ago

Whilst working on #102 I noticed that when given multiple Hi-C samples, the pipeline was only generating a contact map for the first of them. It's because the channel of the genome was a queue channel, not a value channel, meaning that the only value it had was consumed and could not be used for the second sample. I simply added a first to make it a value channel, and the pipeline now generates a contact map for each specimen.

Thanks to this, we can now test CRAM and BAM at the same time, although I personally find testing BAM is redundant with CRAM and I would recommend removing it.

PR checklist

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github-actions[bot] commented 11 months ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 4d8e6df

+| ✅ 132 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

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muffato commented 11 months ago

A single HiC sample is used to generate genome, so why would we want to generate two HiC maps for separate samples. I do not understand the biological use case.

For some species there are multiple HiC libraries from different individuals, sometimes from different strains / populations because we want to explicitly look at how the karyotype structure changes between individuals.

The small change here simply allows generating their contact maps in the same pipeline run, which is slightly more efficient than running the pipeline multiple times.

muffato commented 7 months ago

Closing in favour of #112

sanger-tol / genomenote