Template and module updating #58

gq1 · 2023-09-21T17:23:49Z

PR checklist

This comment contains a description of changes (with reason).
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 pipeline conventions in the contribution docs
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
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).

* TEMPLATE: Template update for nf-core/tools version 2.8 add pipeline template file # Conflicts: # .github/workflows/sanger_test.yml # .github/workflows/sanger_test_full.yml # .nf-core.yml # CHANGELOG.md # CITATIONS.md # LICENSE # README.md # assets/email_template.html # bin/check_samplesheet.py # docs/output.md # docs/usage.md # lib/WorkflowMain.groovy # modules.json # nextflow.config # pipeline_template.yml # workflows/variantcalling.nf

nf-core modules update deepvariant nf-core modules update custom/dumpsoftwareversions nf-core modules update cat/cat nf-core modules update bcftools/concat nf-core lint --fix files_unchanged ( nf-core 2.8)

github-actions · 2023-09-21T17:24:02Z

This PR is against the `main` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @gq1,

It looks like this pull-request is has been made against the sanger-tol/variantcalling main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the sanger-tol/variantcalling dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2023-09-21T17:25:17Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit fe45c30

+| ✅ 126 tests passed       |+
#| ❔  26 tests were ignored |#

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-variantcalling_logo_light.png
files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_light.png
files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-variantcalling_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/variantcalling/variantcalling/.github/workflows/awstest.yml
multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: lib/WorkflowVariantcalling.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-variantcalling_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: '1.1.0-dev'
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (76 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2023-09-26 16:28:39

gq1 · 2023-09-21T17:26:21Z

@sanger-tolsoft fix linting

gq1 · 2023-09-21T17:28:11Z

@nf-core-bot fix linting

sanger-tolsoft · 2023-09-21T17:52:15Z

@nf-core-bot fix linting

sanger-tolsoft · 2023-09-21T17:54:16Z

@nf-core-bot fix linting

priyanka-surana

One minor change. Otherwise all good. 👍

priyanka-surana · 2023-09-26T11:53:02Z

tower.yml

@@ -0,0 +1,3 @@
+reports:
+  samplesheet.csv:
+    display: "Auto-created samplesheet with collated metadata and FASTQ paths"


Update display text.

tests failing

priyanka-surana · 2023-09-26T15:44:16Z

The singularity tests are failing for deepvariant. This is not the case in modules repo, so it is some specific to our pipeline.

Pulling Singularity image docker://nf-core/deepvariant:1.5.0 [cache /lustre/scratch123/tol/teams/tolit/users/ps22/bin/singularity/nf-core-deepvariant-1.5.0.img]
ERROR ~ Error executing process > 'SANGERTOL_VARIANTCALLING:VARIANTCALLING:DEEPVARIANT_CALLER:DEEPVARIANT (3)'

Caused by:
  Failed to pull singularity image
  command: singularity pull  --name nf-core-deepvariant-1.5.0.img.pulling.1695729700476 docker://nf-core/deepvariant:1.5.0 > /dev/null
  status : 255
  message:
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for docker://nf-core/deepvariant:1.5.0: reading manifest 1.5.0 in docker.io/nf-core/deepvariant: errors:
    denied: requested access to the resource is denied
    unauthorized: authentication required

gq1 · 2023-09-26T16:00:41Z

Manually pulling the image works with 6G memory not with 4G memory:
singularity pull --name nf-core-deepvariant-1.5.0.img.pulling.1695743033413 docker://quay.io/nf-core/deepvariant:1.5.0

nextflow.config

priyanka-surana

All tests working. Yay 💃🏼

gq1 added 17 commits September 20, 2023 11:31

nf-core lint --fix files_unchanged ( nf-core 2.8)

febbcff

nf-core modules update bcftools/concat

5fc66d6

nf-core modules update cat/cat

3c7c11a

nf-core modules update custom/dumpsoftwareversions

bed2298

nf-core modules update deepvariant

c9b4e23

add pipeline template file

7789085

Template update for nf-core/tools version 2.8

7a3aeb8

Modules updating:

2ddb943

nf-core modules update deepvariant nf-core modules update custom/dumpsoftwareversions nf-core modules update cat/cat nf-core modules update bcftools/concat nf-core lint --fix files_unchanged ( nf-core 2.8)

update the version to 1.1.0-dev

e54a47a

missing bracks

7d65f86

update the workflow because deepvaritant module updated.

20062b4

nf-core modules update samtools/view

9a8be90

update samtools view workflow because module updated

a4f7033

nf-core modules update samtools/faidx

048d08f

update workflow because samtools faidx module updated

555bc3d

use version 2.8 for nf-core lint in github

6c4804b

gq1 changed the base branch from main to dev September 21, 2023 17:24

gq1 added 2 commits September 21, 2023 18:30

remove white space

07716c2

prettier

9e731d7

gq1 requested a review from priyanka-surana September 21, 2023 17:37

to fail prettier

b302172

[automated] Fix linting with Prettier

d50080e

priyanka-surana previously approved these changes Sep 26, 2023

View reviewed changes

priyanka-surana reviewed Sep 26, 2023

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nextflow.config Show resolved Hide resolved

priyanka-surana and others added 2 commits September 26, 2023 17:24

Update nextflow.config

f5a1186

update the display text.

fe45c30

priyanka-surana approved these changes Sep 26, 2023

View reviewed changes

gq1 merged commit b3d806c into dev Sep 26, 2023
6 checks passed

gq1 deleted the template_merge branch September 26, 2023 16:38

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Template and module updating #58

Template and module updating #58

gq1 commented Sep 21, 2023

github-actions bot commented Sep 21, 2023

github-actions bot commented Sep 21, 2023 •

edited

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❔ Tests ignored:

✅ Tests passed:

Run details

gq1 commented Sep 21, 2023

gq1 commented Sep 21, 2023

sanger-tolsoft commented Sep 21, 2023

sanger-tolsoft commented Sep 21, 2023

priyanka-surana left a comment

priyanka-surana Sep 26, 2023

priyanka-surana commented Sep 26, 2023

gq1 commented Sep 26, 2023

priyanka-surana left a comment

Template and module updating #58

Template and module updating #58

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gq1 commented Sep 21, 2023

PR checklist

github-actions bot commented Sep 21, 2023

This PR is against the main branch ❌

github-actions bot commented Sep 21, 2023 • edited Loading

nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

gq1 commented Sep 21, 2023

gq1 commented Sep 21, 2023

sanger-tolsoft commented Sep 21, 2023

sanger-tolsoft commented Sep 21, 2023

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priyanka-surana Sep 26, 2023

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priyanka-surana commented Sep 26, 2023

gq1 commented Sep 26, 2023

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This PR is against the `main` branch ❌

github-actions bot commented Sep 21, 2023 •

edited

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`nf-core lint` overall result: Passed ✅