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Update centrifuge/centrifuge #1495

Merged
merged 11 commits into from
Apr 7, 2022
Merged

Update centrifuge/centrifuge #1495

merged 11 commits into from
Apr 7, 2022

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sofstam
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@sofstam sofstam commented Apr 5, 2022

This PR fixes one subcommand per module (centrifuge/centrifuge)

PR checklist

Closes #833

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@sofstam sofstam requested a review from jfy133 April 5, 2022 10:35
@sofstam sofstam marked this pull request as draft April 5, 2022 10:57
@sofstam sofstam marked this pull request as ready for review April 6, 2022 15:24
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sofstam commented Apr 6, 2022

I updated the db_name. When I untar the minigut_cf.tar.gz, I get the following files (I think it is a bit strange, if I untar the files locally, I do not get any filenames starting with ._)

minigut_cf/._minigut_cf.4.cf
minigut_cf/minigut_cf.4.cf
minigut_cf/._minigut_cf.1.cf
minigut_cf/minigut_cf.1.cf
minigut_cf/._minigut_cf.2.cf
minigut_cf/minigut_cf.2.cf
minigut_cf/._minigut_cf.3.cf
minigut_cf/minigut_cf.3.cf

That is why I added -not -name "._*" as well.

@jfy133 jfy133 self-requested a review April 7, 2022 07:34
jfy133
jfy133 approved these changes Apr 7, 2022
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I think this looks good now, once we remove a bit of debugging stuff!

(Hopefully the last time we have to update this 😏 )

modules/centrifuge/centrifuge/main.nf Outdated
@@ -31,7 +29,7 @@ process CENTRIFUGE {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def db_name = db.toString().replace(".tar.gz","")
//def db_name = db.toString().replace(".tar.gz","")
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Suggested change
//def db_name = db.toString().replace(".tar.gz","")

If not being used

tests/modules/centrifuge/centrifuge/main.nf Outdated Show resolved Hide resolved
tests/modules/centrifuge/centrifuge/main.nf
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
db = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
db_name = "minigut_cf"
//db_name = "minigut_cf"
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Suggested change
//db_name = "minigut_cf"

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I will update the PR.

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This is still present?

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No, it is not.

jfy133
jfy133 reviewed Apr 7, 2022
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One last thing as I did a final check (then you can merge) nee dto update meta.yml to say input DB is just a directory, not the TAR.GZ!

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sofstam commented Apr 7, 2022

I updated the meta.yml file as well.

@sofstam sofstam merged commit d2726fc into nf-core:master Apr 7, 2022
@sofstam sofstam deleted the centrifuge_centrifuge branch April 7, 2022 10:11
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new module: centrifuge
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@sofstam @jfy133