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Sentieon dedup #3224

Merged
merged 34 commits into from
Mar 30, 2023
Merged

Sentieon dedup #3224

merged 34 commits into from
Mar 30, 2023

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asp8200
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@asp8200 asp8200 commented Mar 30, 2023 •
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Adding module for Sentieons dedup function.

The tests should be passing now.

Also some minor changes to the Sentieon-bwamem module.

  • 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
  • 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. (No, we are getting the docker-image from dockerHub)
  • 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 (Can't be tested with conda)

asp8200 and others added 4 commits March 30, 2023 18:17
@asp8200
Removing option rmdup from test yaml
95af42e
@asp8200 @maxulysse
Update tests/modules/nf-core/sentieon/dedup/nextflow.config
8c36d9a 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@asp8200 @maxulysse
Update modules/nf-core/sentieon/dedup/main.nf
e6cd688 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@asp8200 @maxulysse
Update modules/nf-core/sentieon/dedup/main.nf
41aa5f2 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@asp8200 @maxulysse
Update modules/nf-core/sentieon/bwamem/main.nf
208e3b0 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
asp8200 and others added 11 commits March 30, 2023 18:29
@asp8200 @maxulysse
Update modules/nf-core/sentieon/dedup/main.nf
9087f69 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@asp8200 @maxulysse
Update modules/nf-core/sentieon/dedup/main.nf
9729998 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@asp8200 @maxulysse
Update modules/nf-core/sentieon/dedup/main.nf
dd2e387 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@asp8200 @maxulysse
Update modules/nf-core/sentieon/dedup/main.nf
77e34ca 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@asp8200 @maxulysse
Update modules/nf-core/sentieon/dedup/main.nf
e6f4cad 
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@asp8200
Adding prefix for stub
c5a18fc
@asp8200
fix
12c564a
@asp8200
fix
d26f187
@asp8200
fix
a00e480
@asp8200
Updating md5sums
b26cbb5
@asp8200
Merge branch 'master' into sentieon_dedup
cbba4dd
@asp8200 asp8200 changed the title DRAFT: Sentieon dedup Sentieon dedup Mar 30, 2023
@maxulysse maxulysse added this pull request to the merge queue Mar 30, 2023
Merged via the queue into master with commit 8c159eb Mar 30, 2023
jvfe pushed a commit to jvfe/modules that referenced this pull request Mar 30, 2023
@asp8200 @maxulysse @jvfe
Sentieon dedup (nf-core#3224)
c8bbd5f 
* Fixing stub

* Adding Sentieon-Dedup module and test

* Skipping conda for all tests tagged sentieon

* Adding test for sentieon-dedup

* Not running conda test for sentieon modules

* WIP: Trying to hardcode output to cram

* Fixing suffix

* WIP: Fetch md5sums

* Updating md5sums

* Removing outdated comments

* Adding extra args for driver, LocusCollector and Dedup

* yml-doc for Dedup-module

* Adding updating for rmdup in test-config

* WIP: Adding test for dedup rmdup

* Removing unwanted tags

* Trying to run two dedup-tests

* Adding test of sentieon dedup with removal of reads

* Re-adding secrets

* Removing option rmdup from test yaml

* Update tests/modules/nf-core/sentieon/dedup/nextflow.config

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update modules/nf-core/sentieon/dedup/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update modules/nf-core/sentieon/dedup/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update modules/nf-core/sentieon/bwamem/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update modules/nf-core/sentieon/dedup/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update modules/nf-core/sentieon/dedup/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update modules/nf-core/sentieon/dedup/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update modules/nf-core/sentieon/dedup/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Update modules/nf-core/sentieon/dedup/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

* Adding prefix for stub

* fix

* fix

* fix

* Updating md5sums

---------

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
@muffato muffato deleted the sentieon_dedup branch April 5, 2023 00:22
@edmundmiller
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Closed #734

@asp8200 asp8200 mentioned this pull request Sep 21, 2023
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