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Today, I realized that the container for FASTQSCRE...
# modules
f
Today, I realized that the container for FASTQSCREEN_FASTQSCREEN comes without bismark installed. However, you can run fastscreen in bismark mode when supplying 
--bismark
via 
ext.args
. But then the pipeline will fail, because bismark cannot be found. I worked around by specifying a custom container that I created on Seqera containers. Would you consider this a bug? Or is this expected?
a
IMO if it's an option for the tool then the default container should include it unless it's both • likely rarely used as an option • Presents difficulty in generating a container Given that you are able to create a container for this via seqera containers my personal feeling is that the module should be updated to use that image
👍 1
f
OK, thanks for your feedback! I created a PR https://github.com/nf-core/modules/pull/8758
m
I guess the conda recipe for fastq screen should use bismark as a dependency, no?
a
It would depend on the conda/bioconda rules on optional dependecies I guess (I do not know if there are such rules)
s
I'm fairly sure that #C06PHJM0Y3D are using a different setup for fastqscreen, so you might want to take a look at that too.
a
Hmm seems like @Edmund added a bunch of dependencies as comments but that they aren’t actually in the environment?
f
Yes, adding bismark to conda recipe totally makes sense to me. I updated it to use the same dependencies as the containers I created. These are pretty much the same as in the comments in #C06PHJM0Y3D
Previously, I had updated the container for 
fastqscreen/buildfromindex
as well. But yesterday I realized, that 
fastqscreen/buildfromindex
does actually not need any of these dependencies, it does not even need fastqscreen, because these are simple copy and sed operations.
What is missing right now, is to add tests for bismark aligner. However, that would need quite an update on 
fastqscreen/buildfromindex
, because at the moment this will just build from a bowtie2 index. And we would need a bismark index to add tests for fastqscreen with --bismark. For me, adding buildfromindex for bismark seems out of scope atm, timewise. Do you think adding the updated container/conda recipe without new tests is still useful? Or any idea how to add a test without a new buildfromindex, e.g. by adding a bismark index as test data?
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