Merging template updates #160

Leon-Bichmann · 2021-03-22T11:20:55Z

PR checklist

This comment contains a description of changes (with reason)
CHANGELOG.md is updated
If you've fixed a bug or added code that should be tested, add tests!
Documentation in docs is updated
If necessary, also make a PR on the nf-core/mhcquant branch on the nf-core/test-datasets repo

Leon-Bichmann · 2021-03-23T09:46:18Z

Ok this is ready to be merged, once the bug fix for the nfcore schema is integrated into the template.

Leon-Bichmann · 2021-03-24T09:20:33Z

it seems the last test in the CI doesn't complete even everything is done already:
Run workflow tests Expected — Waiting for status to be reported

ggabernet · 2021-03-24T10:58:13Z

Hey @Leon-Bichmann this needs to be updated under Settings > Branches > Tick or untick the relevant tests. I think you have write rights to the repo so it should work for you as well

ewels

Found a few things, but mostly looking good.

Lots is about the fact that you don't use --genome, but now I get to the end I'm not sure if that's even the case or not 😅 Feel free to ignore if not.

README.md

conf/igenomes.config

conf/test.config

main.nf

nextflow.config

ewels · 2021-03-24T11:02:26Z

nextflow.config

@@ -44,6 +51,10 @@ params {
  variant_snp_filter = false
  outdir = './results'

+  validate_params = true
+  show_hidden_params = false
+  schema_ignore_params = 'genomes,input_paths'


If not using --genome

Suggested change

schema_ignore_params = 'genomes,input_paths'

schema_ignore_params = 'input_paths'

nextflow.config

nextflow_schema.json

Co-authored-by: Phil Ewels <[email protected]>

…chmann/MHCquant into merging-template-updates

Leon-Bichmann · 2021-03-24T16:04:30Z

@ewels - same here everything passed, but I guess I wait to include the 1.13.3 template updates still

…erging-template-updates

ewels

Just the questions about stripping --genome stuff if you're not using it, plus a little schema tidying would be nice, otherwise looks great 👍🏻

nextflow_schema.json

main.nf

+// Check if genome exists in the config file
+if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+    exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(', ')}"
 }


nextflow.config

@@ -44,6 +51,10 @@ params {
  variant_snp_filter = false
  outdir = './results'

+  validate_params = true
+  show_hidden_params = false
+  schema_ignore_params = 'genomes,input_paths'


ewels

Very nearly!

nextflow_schema.json

nextflow.config

Co-authored-by: Phil Ewels <[email protected]>

…chmann/MHCquant into merging-template-updates

ewels

Looking great! Again you've got an empty schema group but I'll sort that out in another PR for you now.

Thanks for your patience 🙏🏻

nf-core-bot and others added 15 commits October 27, 2020 09:25

Template update for nf-core/tools version 1.11

e7456a0

Template update for nf-core/tools version 1.12

9be44f9

Template update for nf-core/tools version 1.12.1

19c919d

Template update for nf-core/tools version 1.13

f633596

Template update for nf-core/tools version 1.13.1

abca6d0

Merged changes from nf-core template

770e2f5

fixes

b9decdd

fixes

3ed7b53

fixes

3992067

change version to dev

dedcb7a

rm config_profile_name

582eeff

final schema and lincence fixes

f4196fa

fix add missing bracket

1f48e6c

rm name from config

7b0c3df

rm .

7cb1567

Leon-Bichmann mentioned this pull request Mar 22, 2021

NfcoreSchema.validateParameters JSONObject error nf-core/tools#937

Closed

Leon-Bichmann added 5 commits March 22, 2021 21:48

rm params.name

f4cf767

fix lib schema and params.name

bca1745

rm costum_runName

c3b14b2

rm costum_runName

0174cf8

change permissions

920c7d0

nf-core-bot and others added 4 commits March 23, 2021 16:06

Template update for nf-core/tools version 1.13.2

d883490

update changelog

e0802e3

merge template update

ebac663

update changelog

9cd11bd

ewels requested changes Mar 24, 2021

View reviewed changes

Leon-Bichmann and others added 11 commits March 24, 2021 15:15

Update README.md

8ed3a3d

Co-authored-by: Phil Ewels <[email protected]>

Update Readme with summary

96b3881

Merge branch 'merging-template-updates' of https://github.com/Leon-Bi…

a26c8a7

…chmann/MHCquant into merging-template-updates

update README with references

0d1d8ef

remaining changes for review

8cb5bce

1.6.1dev

586432c

fix README style

bd22df1

fix README style

659a529

rm igenomes_base

2c3125e

config_profile_name

23f5523

fix README

affbb93

Leon-Bichmann requested a review from ewels March 25, 2021 08:55

nf-core-bot and others added 3 commits March 25, 2021 18:17

Template update for nf-core/tools version 1.13.3

cc502a8

Merge branch 'TEMPLATE' of https://github.com/nf-core/mhcquant into m…

dcede76

…erging-template-updates

update to 1.13.3

dc1a4ad

Leon-Bichmann requested review from ggabernet and apeltzer March 30, 2021 11:53

ewels requested changes Mar 31, 2021

View reviewed changes

fixes schema and rm genomes

0a81da4

ewels requested changes Mar 31, 2021

View reviewed changes

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Leon-Bichmann and others added 5 commits March 31, 2021 19:09

Update nextflow_schema.json

b5f2a47

Co-authored-by: Phil Ewels <[email protected]>

Update nextflow.config

d908d97

Co-authored-by: Phil Ewels <[email protected]>

last removals

c9b3603

Merge branch 'merging-template-updates' of https://github.com/Leon-Bi…

238ae19

…chmann/MHCquant into merging-template-updates

rm aws and cluster options from config

c82b9db

ewels approved these changes Mar 31, 2021

View reviewed changes

ewels merged commit b6c4256 into nf-core:dev Mar 31, 2021

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Merging template updates #160

Merging template updates #160

Leon-Bichmann commented Mar 22, 2021 •

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	schema_ignore_params = 'genomes,input_paths'
	schema_ignore_params = 'input_paths'

Merging template updates #160

Merging template updates #160

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Leon-Bichmann commented Mar 22, 2021 • edited Loading

PR checklist

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Leon-Bichmann commented Mar 22, 2021 •

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