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new module: verifybamid #1957

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4 tasks done
manifestoso opened this issue Aug 18, 2022 · 3 comments · Fixed by #2090
Closed
4 tasks done

new module: verifybamid #1957

manifestoso opened this issue Aug 18, 2022 · 3 comments · Fixed by #2090
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@manifestoso
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new module Adding a new module

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@manifestoso
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Is there an existing module for this?

  • I have searched for the existing module

Is there an open PR for this?

  • I have searched for existing PRs

Is there an open issue for this?

  • I have searched for existing issues

Are you going to work on this?

  • If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module
@manifestoso manifestoso added the new module Adding a new module label Aug 18, 2022
@manifestoso
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I can't assign the ticket. sorry.

manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Aug 18, 2022
@manifestoso
nf-core#1957 - verifybam init +
e1d4ece
manifestoso pushed a commit to NSWHP-Genomics/modules that referenced this issue Aug 19, 2022
nf-core#1957 - verifybamid + verifybamid2 init +
fb53945
@manifestoso manifestoso changed the title new module: verifybamid/contamination new module: verifybamid Sep 8, 2022
@jfy133
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jfy133 commented Sep 8, 2022

If you follow the 'join on github' instructions https://nf-co.re/join you should be able to assign yourself in teh future

This was referenced Sep 8, 2022
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@manifestoso
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If you follow the 'join on github' instructions https://nf-co.re/join you should be able to assign yourself in teh future

Cheers @jfy133 done.

@manifestoso manifestoso mentioned this issue Sep 10, 2022
Merged
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 10, 2022
@manifestoso
nf-core#1957 - including test data from nf-core/test-datasets#603 4 v…
138d544 
…erifybamid2 +
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 20, 2022
@manifestoso
nf-core#1957 - verifybamid2 module with new test_data nf-core/test-da…
4bfb85d 
…tasets#603
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 20, 2022
@manifestoso
nf-core#1957 - VerifyBamID2 module w/t conda + lint
a6baad9
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 22, 2022
@manifestoso
nf-core#1957 - verifybamid2 complete + multi ref enabled fix NSWPH_Ge…
7e40ac2 
…nomics/ToDos-DevOps#15 and fix NSWPH_Genomics/ToDos-DevOps#10
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 22, 2022
@manifestoso
nf-core#1957 - multi pytest pass close NSWPH_Genomics/ToDos-DevOps#3
56b3a65
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 22, 2022
@manifestoso
nf-core#1957 - updated docker image fix NSWPH_Genomics/ToDos-DevOps#4…
ee29dfe 
… + close NSWPH_Genomics/ToDos-DevOps#20
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 22, 2022
@manifestoso
nf-core#1957 - prep 4 PR close NSWPH_Genomics/ToDos-DevOps#21
ee8832c
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 22, 2022
@manifestoso
nf-core#1957 - prep and clean 4 PR close NSWPH_Genomics/ToDos-DevOps#21
ec56973
manifestoso added a commit to NSWHP-Genomics/modules that referenced this issue Sep 22, 2022
@manifestoso
nf-core#1957 - PR branch clean
d47fd33
This was referenced Sep 22, 2022
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manifestoso added a commit that referenced this issue Oct 10, 2022
@manifestoso @jfy133
fix 1957 - new module verifybamid. close NSWHP-Genomics/ToDos-DevOps#39…
52e4f76 
…, close NSWHP-Genomics/ToDos-DevOps#47, close NSWHP-Genomics/ToDos-DevOps#3, close NSWHP-Genomics/ToDos-DevOps#4, close NSWHP-Genomics/ToDos-DevOps#22, close NSWHP-Genomics/ToDos-DevOps#24, close NSWHP-Genomics/ToDos-DevOps#25, close NSWHP-Genomics/ToDos-DevOps#39, close NSWHP-Genomics/ToDos-DevOps#25, close NSWHP-Genomics/ToDos-DevOps#22

fix 1957 - new module verifybamid. close NSWHP-Genomics/ToDos-DevOps#39, close NSWHP-Genomics/ToDos-DevOps#47, close NSWHP-Genomics/ToDos-DevOps#3, close NSWHP-Genomics/ToDos-DevOps#4, close NSWHP-Genomics/ToDos-DevOps#22, close NSWHP-Genomics/ToDos-DevOps#24, close NSWHP-Genomics/ToDos-DevOps#25, close NSWHP-Genomics/ToDos-DevOps#39, close NSWHP-Genomics/ToDos-DevOps#25, close NSWHP-Genomics/ToDos-DevOps#22

* #1957 - verifybam init +

* #1957 - verifybamid + verifybamid2 init +

* #1957 - including test data from nf-core/test-datasets#603 4 verifybamid2 +

* #1957 - verifybamid2 module with new test_data nf-core/test-datasets#603

* #1957 - VerifyBamID2 module w/t conda + lint

* #1957 - verifybamid2 complete + multi ref enabled fix NSWPH_Genomics/ToDos-DevOps#15 and fix NSWPH_Genomics/ToDos-DevOps#10

* #1957 - multi pytest pass close NSWPH_Genomics/ToDos-DevOps#3

* #1957 - updated docker image fix NSWPH_Genomics/ToDos-DevOps#4 + close NSWPH_Genomics/ToDos-DevOps#20

* #1957 - prep 4 PR close NSWPH_Genomics/ToDos-DevOps#21

* #1957 - prep and clean 4 PR close NSWPH_Genomics/ToDos-DevOps#21

* #1957 - PR branch clean

* PR - lint compliance fix NSWHP-Genomics/ToDos-DevOps#22

* PR - lint compliance fix NSWHP-Genomics/ToDos-DevOps#22

* PR - ltest int compliance , rm md5 check path only.fix NSWPH-Genomics/ToDos-DevOps#225

* PR - ltest int compliance , rm md5 check path only.fix NSWHP-Genomics/ToDos-DevOps#25

* header removal modules/verifybamid/verifybamid2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* meta file cosmatics fix modules/verifybamid/verifybamid2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* PR debug - conformance

* PR debug - conformance test

* PR debug - meta reduction to bare min

* PR debug - verifybamid2 flag reduction to bare min

* PR debug - RefVCF flag reduction to bare min

* PR debug - RefVCF flag reduction to bare min

* meta conform modules/verifybamid/verifybamid2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* meta conform modules/verifybamid/verifybamid2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* meta conform modules/verifybamid/verifybamid2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* PR conformance - reduce redundent flags, fix NSWHP-Genomics/ToDos-DevOps#45, close NSWHP-Genomics/ToDos-DevOps#3, close NSWHP-Genomics/ToDos-DevOps#4, close NSWHP-Genomics/ToDos-DevOps#22, close NSWHP-Genomics/ToDos-DevOps#24, close NSWHP-Genomics/ToDos-DevOps#25, close NSWHP-Genomics/ToDos-DevOps#39

* PR fix - meta syntax + cleanup -close NSWHP-Genomics/ToDos-DevOps#39

* PR fix - test cleanup + test include svd test module, fix NSWHP-Genomics/ToDos-DevOps#47

* comments rm modules/verifybamid/verifybamid2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* comments rm modules/verifybamid/verifybamid2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* conformance : nf-core folder structure

* CI trigger

* PR debug - nf-core folder structure upgrade conformance

Co-authored-by: EC2 Default User <ec2-user@ip-10-100-5-110.ap-southeast-2.compute.internal>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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fix #1957 - including new module verifybamid2 NSWHP-Genomics/modules
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@manifestoso @jfy133