release 2.0.0 #144

nservant · 2023-01-04T16:52:56Z

PR checklist

This comment contains a description of changes (with reason).
Make sure your code lints (nf-core lint .).
Ensure the test suite passes (nextflow run . -profile test,docker).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

Ready for the next release of nf-core-hic.
Changes include ;

DSL2 implentation
Add full dataset
Update with the last code template

Dev

sync repo

Update master with template merge

update conda env and markdown typo

update env

mv to python 2.15

firt release

first release

Fix bug in environment

First version DSL2 from nf-core

workflows/hic.nf

maxulysse

Minor changes are needed for the release (thinking mainly about the correct zenodo link, and dealing with the environment.yml).
The rest can probably wait a bit, but should be easy to squeeze in.

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

@maxulysse

inline channel build as suggested by @maxulysse

drpatelh · 2023-01-09T11:10:28Z

We should release this as 2.0! 🚀

maxulysse

I think @drpatelh has a good point about the release being 2.0 instead of 1.4.0.
Apart from that weems ok to me, I'll be running the megatests to make sure that the new release works well with tower/AWS.

nservant · 2023-01-09T14:58:55Z

agree for version 2.0 !
Should I did the changes on my own dev branch, then, re-open a new PR to the nf-core-hic/dev ?

maxulysse · 2023-01-09T15:08:40Z

agree for version 2.0 ! Should I did the changes on my own dev branch, then, re-open a new PR to the nf-core-hic/dev ?

I think that's the proper way to do modifications ;-)

nservant · 2023-01-11T08:30:25Z

@drpatelh, @maxulysse, I created a new PR to bump v2.0.0
#145

[BUMP] v2.0.0

maxulysse · 2023-01-16T10:27:32Z

@nservant regarding the
Argument of 'channel.from' method cannot be a channel object — Likely you can replace the use of 'channel.from' with the channel object itself
You'll have to replace channel.from by channel.of, cf nf-core/sarek#906

Remove usages of deprecated Channel.from method

maxulysse

<3

robsyme · 2023-01-19T16:05:07Z

Maxime (and perhaps others) have noted that the hic pipeline is generating the warning

WARN: A process with name 'BOWTIE2_ALIGN_TRIMMED' is defined more than once in module script: /home/runner/work/hic/hic/./workflows/../subworkflows/local/./hicpro_mapping.nf -- Make sure to not define the same function as process

This looks like a bug in Nextflow for which I have filed an issue (nextflow-io/nextflow#3560). A workaround would be to ensure that both imports of the BOWTIE2_ALIGN process are aliased to new names.

edmundmiller

Looks great to me! A few things I found, but nothing major.

environment.yml

modules/local/hicpro/get_valid_interaction_dnase.nf

nextflow_schema.json

subworkflows/local/cooler.nf

subworkflows/local/hicpro.nf

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

nservant and others added 30 commits April 19, 2019 19:26

Merge pull request #7 from nservant/dev

8b46e84

Dev

Merge branch 'master' of https://github.com/nservant/nf-core-hic

ac87841

Merge pull request #9 from nf-core/master

b54f1cc

sync repo

Merge pull request #12 from nservant/dev

1941bb5

Update master with template merge

Merge pull request #13 from nservant/dev

9cb7d76

update conda env and markdown typo

Merge pull request #15 from nservant/dev

1ba48c4

update env

Merge pull request #16 from nservant/dev

f6002d0

mv to python 2.15

Merge pull request #19 from nservant/dev

52ea795

firt release

Merge pull request #21 from nf-core/master

c0e6b9e

first release

Merge branch 'master' of https://github.com/nf-core/nf-core-hic

e66b4e8

Merge branch 'master' of https://github.com/nf-core/nf-core-hic

926fdbf

update CHANGELOG

2f2cc1e

[MERGE] dev nf-core

c738afc

Merge branch 'master' of https://github.com/nf-core/nf-core-hic

3386374

Template update for nf-core/tools version 2.0

7395bac

Template update for nf-core/tools version 2.0.1

4565ea5

Template update for nf-core/tools version 2.1

2211520

Merge branch 'dev' of https://github.com/nservant/nf-core-hic

a621078

[BUG] fix cooltools env #109

9f47a54

[BUMP] v1.3.1

4ba16ef

Merge pull request #110 from nservant/dev

66f1b55

Fix bug in environment

First version DSL2 from nf-core

1999c0d

Merge pull request #24 from philippelarosa/dsl2

8e58e39

First version DSL2 from nf-core

Template update for nf-core/tools version 2.2

d7a1e34

[MODIF] init DSL2

c386dd1

[MODIF] init DSL2

e25fd4d

[MODIF] HICPRO workflow is running

48c932d

[MODIF] add cooler subworkflow

33572cf

[DSL2] add merge_stats

dda1608

[MODIF] update cooltools

f17ea6f

maxulysse reviewed Jan 5, 2023

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maxulysse reviewed Jan 5, 2023

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maxulysse requested changes Jan 6, 2023

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nservant and others added 3 commits January 6, 2023 18:16

Update zenodo links

86999cd

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

Update workflows/hic.nf

262c90a

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

Update hic.nf

9b7e196

inline channel build as suggested by @maxulysse

nservant requested a review from maxulysse January 6, 2023 17:35

maxulysse approved these changes Jan 9, 2023

View reviewed changes

[BUMP] v2.0.0

99db21c

nservant mentioned this pull request Jan 11, 2023

[BUMP] v2.0.0 #145

Merged

nservant added 2 commits January 13, 2023 13:55

[HICPRO] update c++ complilation

90f8469

Merge pull request #145 from nservant/dev

0f1ff36

[BUMP] v2.0.0

nservant changed the title ~~release 1.4.0~~ release 2.0.0 Jan 16, 2023

nservant and others added 2 commits January 16, 2023 21:42

[BUG] fix bug in channel.from

4de40e3

Merge pull request #146 from nservant/dev

ac48a44

Remove usages of deprecated Channel.from method

maxulysse approved these changes Jan 17, 2023

View reviewed changes

edmundmiller self-requested a review January 19, 2023 16:02

edmundmiller approved these changes Jan 19, 2023

View reviewed changes

nservant and others added 5 commits January 20, 2023 15:18

Update modules/local/hicpro/get_valid_interaction_dnase.nf

c3b76f9

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

Update subworkflows/local/cooler.nf

f720ed5

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

Update nextflow_schema.json

a695092

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

Update nextflow_schema.json

ea97a90

Update nextflow_schema.json

f960b38

nservant merged commit b4d89cf into master Jan 21, 2023

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release 2.0.0 #144

release 2.0.0 #144

nservant commented Jan 4, 2023

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drpatelh commented Jan 9, 2023

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nservant commented Jan 9, 2023

maxulysse commented Jan 9, 2023

nservant commented Jan 11, 2023 •

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maxulysse commented Jan 16, 2023

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release 2.0.0 #144

release 2.0.0 #144

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nservant commented Jan 4, 2023

PR checklist

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nservant commented Jan 11, 2023 • edited Loading

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nservant commented Jan 11, 2023 •

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