Important! Template update for nf-core/tools v1.10.2

[nf-core-bot]

A new release of the main template in nf-core/tools has just been released. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible. Once complete, make a new minor release of your pipeline. For instructions on how to merge this PR, please see https://nf-co.re/developers/sync.

For more information about this release of nf-core/tools, please see the nf-core/tools v1.10.2 release page.

[maxulysse]

I'm on it, since there's many conflicts to resolve

[ggabernet]

Hey @maxulysse , as far as I know there will be very soon the 10.1.2 patch release, so maybe it's better to wait for this one?

[maxulysse]

Hey @maxulysse , as far as I know there will be very soon the 10.1.2 patch release, so maybe it's better to wait for this one?

I'm guessing the 10.1.2 will add minor changes to this one, so it's either a big chunk now and a tiny later, or a big + tiny all at once.

I would say that the total effort should amount to the same in the end

[maxulysse]

I retract whatever I was saying before.

[ggabernet]

Can't say I didn't warn you! 😂

[maxulysse]

Luckily, other stuff happened, and I did not progress much with the conflicts

[github-actions]

nf-core lint overall result: Failed ❌

Posted for pipeline commit 4d88179

+| ✅ 56 tests passed       |+
!| ❗  0 tests had warnings |!
-| ❌  1 tests failed       |-

❌ Test failures:

• Test #4 - Config variable (incorrectly) found: params.igenomesIgnore

✅ Tests passed:

• Test #1 - File found: nextflow.config
• Test #1 - File found: nextflow_schema.json
• Test #1 - File found: Dockerfile
• Test #1 - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• Test #1 - File found: README.md
• Test #1 - File found: CHANGELOG.md
• Test #1 - File found: docs/README.md
• Test #1 - File found: docs/output.md
• Test #1 - File found: docs/usage.md
• Test #1 - File found: .github/workflows/branch.yml
• Test #1 - File found: .github/workflows/ci.yml
• Test #1 - File found: .github/workflows/linting.yml
• Test #1 - File found: main.nf
• Test #1 - File found: environment.yml
• Test #1 - File found: conf/base.config
• Test #1 - File found: .github/workflows/awstest.yml
• Test #1 - File found: .github/workflows/awsfulltest.yml
• Test #1 - File not found check: Singularity
• Test #1 - File not found check: parameters.settings.json
• Test #1 - File not found check: .travis.yml
• Test #3 - Licence check passed
• Test #2 - Dockerfile check passed
• Test #4 - Config variable found: manifest.name
• Test #4 - Config variable found: manifest.nextflowVersion
• Test #4 - Config variable found: manifest.description
• Test #4 - Config variable found: manifest.version
• Test #4 - Config variable found: manifest.homePage
• Test #4 - Config variable found: timeline.enabled
• Test #4 - Config variable found: trace.enabled
• Test #4 - Config variable found: report.enabled
• Test #4 - Config variable found: dag.enabled
• Test #4 - Config variable found: process.cpus
• Test #4 - Config variable found: process.memory
• Test #4 - Config variable found: process.time
• Test #4 - Config variable found: params.outdir
• Test #4 - Config variable found: params.input
• Test #4 - Config variable found: manifest.mainScript
• Test #4 - Config variable found: timeline.file
• Test #4 - Config variable found: trace.file
• Test #4 - Config variable found: report.file
• Test #4 - Config variable found: dag.file
• Test #4 - Config variable found: process.container
• Test #4 - Config variable (correctly) not found: params.version
• Test #4 - Config variable (correctly) not found: params.nf_required_version
• Test #4 - Config variable (correctly) not found: params.container
• Test #4 - Config variable (correctly) not found: params.singleEnd
• Test #4 - Config timeline.enabled had correct value: true
• Test #4 - Config report.enabled had correct value: true
• Test #4 - Config trace.enabled had correct value: true
• Test #4 - Config dag.enabled had correct value: true
• Test #4 - Config manifest.name began with nf-core/
• Test #4 - Config variable manifest.homePage began with https://github.com/nf-core/
• Test #4 - Config dag.file ended with .svg
• Test #4 - Config variable manifest.nextflowVersion started with >= or !>=
• Test #4 - Config process.container looks correct: nfcore/sarek:dev
• Test #4 - Config manifest.version ends in dev: '3.0dev'

Run details:

• nf-core/tools version 1.10.2
• Run at 2020-07-31 14:06:36