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Fix falco
sample names
#7394
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Fix falco
sample names
#7394
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Symlinks are now created as in other modules to make sure that the reported sample names are affected by the value of `prefix`. This makes it easier to use `falco` in `MultiQC` reports.
You'll need to regenerate the test snapshots ( |
Using Docker this time since the only CI test failing are those using Docker...
@SPPearce do you have any idea why
It is clearly related with the tests not passing since the tests fail with singularity when I generate the snapshot with Docker and vice-versa. I used the same tag for both containers, so the reason of this error is unclear to me. |
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I'm on my phone and GitHub thinks I have an unfinished review, not sure what that actually contains.
No, I don't see why it would be complaining, my first thought would be that the conda definition in the environment.yml would be different, but that isn't the case. They all look in sync to me
'biocontainers/falco:1.2.1--h867801b_3' }" | ||
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container | ||
? 'https://depot.galaxyproject.org/singularity/falco:1.2.5--h077b44d_0' | ||
: 'biocontainers/falco:1.2.5--h077b44d_0'}" |
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: 'biocontainers/falco:1.2.5--h077b44d_0'}" | |
: 'biocontainers/falco:1.2.5--h077b44d_0' }" |
Could it potentially be this space not being there?
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I tried with and without the space, with an additional new line, and nothing changes.
Actually, using the initial version of the module (1.2.1
) yields the same result.
There is something iffy here... 🤔
Hi 👋
This PR modifies the definition of the
falco
module so that the reported sample names are affected by the value of theprefix
variable instead of the actual input file name.To achieve this, it simply uses the same strategy as many other modules: Symlinks are now created to provide input files named after the desired
prefix
.This makes it easier to include
falco
output inMultiQC
reports.In the meantime, I also updated the value of
falco
form1.2.1
to1.2.5
.