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# genephylo
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    (part of) team okinawa
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  • c
    Simplest nf-test assertion:
    Copy code
    assertAll(
                { assert process.success },
                { assert snapshot(process.out).match() }
            )
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    @Lea Picard (leapfroggie_) In 
    ~/.nextflow/config
    you can try to set 
    singularity.cacheDir
    to somewhere that the compute nodes can write, like somewhere in 
    /apps/unit/YamamotoU/
    .
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  • p
    おはようございます 😂
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    I made a temporary branch for holding test data until it moves to a more proper place. https://github.com/nf-core/genephylo/tree/tmpBranch_forTestData
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  • p
    should I move the test data for treerecs there? We got this comment from the review :"These neeed to be copied over to nf-core/testdatasets, so we can keep 'control' over them and are not deleted by or moved by someone else 1"
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    @Patricia Muskus I made PR to nf-core/testdatasets! https://github.com/nf-core/test-datasets/pull/1918 Also, Charles suggested me to use established data in test-datasets. This is because we have no reason to use sample data, if we can find good data in it.
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    For treerecs you'll have to push to test-datasets though because it's very specific and I doubt any fitting data exist for it
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    <!subteam^S016E36N7TQ> sorry to bother you guys but I realized the pipeline doesn't show on the website, is there anything specific I need to do for that? Should I wait until we have a v1 ready?
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    +2
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    @藤田隆弘 could you run test on treerecs? It is failing on my side but I can't figure out why
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    i just pushed it
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    @Patricia Muskus OK!
  • p
    thank you 😅
  • u
    @Patricia Muskus It is said that in 
    path(smap) , optional: true
    in line 12, 
    , optional: true
    in not needed so I'm trying without it
  • p
    I tried that too, removing optional:true but it still failed
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    not sure why...
  • u
    It accepted with Test one, not stub! So there should be some other errors in stub. Also, 
    path "versions.yml", emit: versions
    is the old way to emit version so I'll fix it (from nextflow version 3.5, it changed it!)
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  • c
    eval $(ssh-agent) ; ssh-add
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    @Patricia Muskus I pushed it and it still not works in stub.
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    I have tried changing stub to match input
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    but that still did not work
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    @Patricia Muskus ChatGPT said that they could not get version number. 
    tuple val("${task.process}"), val("treerecs"), eval("treerecs --version | sed -n 's/.*(\([0-9.]*\)).*/\1/p'"), emit: versions_treerecs, topic: versions
    This code stands for emitting version number. Inside eval, First call treerecs app and make them output version. Second, beyond 
    sed
    , it cuts out information that bothering. There could be mistake in this sentence, especially inside sed, so I'm trying to fix it now
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  • c
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    ご苦労さまでした
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    @Lea Picard (leapfroggie_) Finished pushing macse refinealignment into master! https://github.com/nf-core/modules/pull/10586
    deal with it parrot 1
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