diamond blastx subworkflow #74

alxndrdiaz · 2023-06-06T01:11:54Z

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).

github-actions · 2023-06-06T01:13:26Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 751c07c

+| ✅ 129 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
nextflow_config - Config manifest.version should end in dev: '0.2.0'

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
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/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/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-blobtoolkit_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-blobtoolkit_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-blobtoolkit_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml

✅ 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: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.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: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: lib/WorkflowBlobtoolkit.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-blobtoolkit_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 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/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html 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
readme - README Nextflow minimum version badge matched config. Badge: 23.04.1, Config: 23.04.1
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 (113 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: sangertest.yml
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: sangerfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2023-09-17 10:23:27

alxndrdiaz · 2023-06-06T01:13:40Z

Small test works: nextflow run . -profile test,docker --outdir <OUTDIR>, and files to run the full test were also added

priyanka-surana

How does this result get merged into the blobdir?

conf/test_full.config

hs_err_pid20966.log

conf/modules.config

modules/local/blobtoolkit/chunk_busco.nf

modules/local/blobtoolkit/unchunk_blastx.nf

replay_pid20966.log

subworkflows/local/run_diamond_blastx.nf

workflows/blobtoolkit.nf

priyanka-surana · 2023-06-07T12:29:22Z

When I run the test profile, I get the following warning.

WARN: Found unexpected parameters:
* --uniprot_blastx: /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit/assets/test/mCerEla1.1.buscoregions.dmnd
- Ignore this warning: params.schema_ignore_params = "uniprot_blastx"

I think modifying the schema and config should fix it.

conf/test.config

modules/local/blobtoolkit/chunk.nf

workflows/blobtoolkit.nf

priyanka-surana · 2023-06-19T10:47:34Z

Almost there, just a few small changes.

change uniprot database names Co-authored-by: Priyanka Surana <[email protected]>

Co-authored-by: Priyanka Surana <[email protected]>

This reverts commit 49cb8bf.

alxndrdiaz · 2023-09-19T16:05:26Z

@priyanka-surana Just want to confirm if this can be merged, the requested change should be resolved in this commit: 8f3f719. If there are no other changes it can be merged.

priyanka-surana · 2023-12-16T17:17:33Z

Closing and opening a fresh PR. Give a couple days.

Alexander Ramos-Diaz and others added 6 commits May 23, 2023 02:33

added chunk_busco module

b2e2e06

added diamond_blastx module

a833404

added blastx_cols and blastx_outext

94b44c9

fix DIAMOND_BLASTX path

46ae681

added module BLOBTOOLKIT_UNCHUNK

b5594c4

diamond_blastx data for test_full

4c3e944

alxndrdiaz requested a review from priyanka-surana June 6, 2023 01:11

alxndrdiaz self-assigned this Jun 6, 2023

alxndrdiaz added the enhancement Improvement of the existing features label Jun 6, 2023

alxndrdiaz added this to the 0.2.0 milestone Jun 6, 2023

alxndrdiaz linked an issue Jun 6, 2023 that may be closed by this pull request

subworkflow: diamond_blastx #20

Closed

priyanka-surana suggested changes Jun 6, 2023

View reviewed changes

priyanka-surana modified the milestones: 0.2.0, 0.1.0 Jun 6, 2023

alxndrdiaz and others added 9 commits June 7, 2023 19:47

removed log files

40c212a

fix path to uniprot_blastx

0ae6480

renamed files in RUN_BLASTX subworkflow

a7502f0

use meta and meta2

8de106a

use names in RUN_BLASTX input channels

5466144

added uniprot_blastx

d667473

merge blastx results in BlobDir

49cb8bf

minimum Nextflow version 23.04.1

abc2b97

update uniprot databases

7bd7873

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updated paths to uniprot databases

cec0022

priyanka-surana suggested changes Jun 19, 2023

View reviewed changes

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alxndrdiaz and others added 10 commits June 19, 2023 10:17

Update conf/test.config

ddb9645

change uniprot database names Co-authored-by: Priyanka Surana <[email protected]>

use new names for uniprot databases

d814e5f

Update modules/local/blobtoolkit/chunk.nf

3bc14aa

Co-authored-by: Priyanka Surana <[email protected]>

update names for uniprot databases

72f040c

fix description

0dbc9b6

update uniprot database names

c8bef6c

check params.blastp and params.blastx

1c9f9c4

independent channels in RUN_BLASTX

8f3f719

RUN_BLASTX subworkflow description

d21e11d

added RUN_BLASTX versions

6c5e052

priyanka-surana changed the base branch from dev to release July 1, 2023 07:00

priyanka-surana added 2 commits September 17, 2023 10:57

Revert "merge blastx results in BlobDir"

524f81b

This reverts commit 49cb8bf.

add update blobdir for blastx

751c07c

muffato added the no_remind label Oct 24, 2023

priyanka-surana closed this Dec 16, 2023

priyanka-surana deleted the diamond_blastx branch December 16, 2023 17:25

priyanka-surana restored the diamond_blastx branch December 16, 2023 18:53

priyanka-surana deleted the diamond_blastx branch December 16, 2023 19:08

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diamond blastx subworkflow #74

diamond blastx subworkflow #74

alxndrdiaz commented Jun 6, 2023

github-actions bot commented Jun 6, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

alxndrdiaz commented Jun 6, 2023

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priyanka-surana commented Jun 7, 2023

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priyanka-surana commented Jun 19, 2023

alxndrdiaz commented Sep 19, 2023

priyanka-surana commented Dec 16, 2023

diamond blastx subworkflow #74

diamond blastx subworkflow #74

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alxndrdiaz commented Jun 6, 2023

PR checklist

github-actions bot commented Jun 6, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

alxndrdiaz commented Jun 6, 2023

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priyanka-surana commented Jun 7, 2023

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priyanka-surana commented Jun 19, 2023

alxndrdiaz commented Sep 19, 2023

priyanka-surana commented Dec 16, 2023

github-actions bot commented Jun 6, 2023 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️