Fasta align dedup bwameth #475

sateeshperi · 2024-11-30T08:15:17Z

closes #467

…lved

github-actions · 2024-11-30T08:17:23Z

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

Posted for pipeline commit 8c62106

+| ✅ 201 tests passed       |+
#| ❔   5 tests were ignored |#

❔ Tests ignored:

files_exist - File is ignored: lib/nfcore_external_java_deps.jar
files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: .github/workflows/ci.yml
actions_ci - actions_ci
modules_config - modules_config

✅ 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: 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/config.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/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: assets/nf-core-methylseq_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-methylseq_logo_light.png
files_exist - File found: docs/images/nf-core-methylseq_logo_dark.png
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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-methylseq_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowMethylseq.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
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: manifest.homePage
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
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: 2.8.0dev
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.aligner= bismark
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.nextseq_trim= 0
nextflow_config - Config default value correct: params.num_mismatches= 0.6
nextflow_config - Config default value correct: params.no_overlap= true
nextflow_config - Config default value correct: params.ignore_r1= 0
nextflow_config - Config default value correct: params.ignore_r2= 2
nextflow_config - Config default value correct: params.ignore_3prime_r1= 0
nextflow_config - Config default value correct: params.ignore_3prime_r2= 2
nextflow_config - Config default value correct: params.use_gpu= false
nextflow_config - Config default value correct: params.min_depth= 0
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/methylseq
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml 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 - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-methylseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-methylseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-methylseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.10.2, Config: 24.10.2
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 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: nf-test.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test-gpu.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - PRESEQ_LCEXTRAP found in conf/base.config and Nextflow scripts.
base_config - BISMARK_ALIGN found in conf/base.config and Nextflow scripts.
base_config - BISMARK_DEDUPLICATE found in conf/base.config and Nextflow scripts.
base_config - BISMARK_METHYLATIONEXTRACTOR found in conf/base.config and Nextflow scripts.
base_config - BWAMETH_ALIGN found in conf/base.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2

Run details

nf-core/tools version 3.0.2
Run at 2024-12-12 02:01:20

sateeshperi · 2024-11-30T09:11:25Z

The difference in md5 of samtools stats output is due to the input now being a sorted bam, rather than raw aligned unsorted bam

…v vars and excluded cancelled from confirm-pass

CI: add gpu tag test job

conf/modules/parabricks_fq2bammeth.config

nextflow.config

subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf

subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test

sateeshperi added 5 commits November 30, 2024 07:36

install subworkflows/nf-core/fastq_align_dedup_bwameth/

828db02

plug into methylseq and create conf/subworkflows

cb71a6e

add use_gpu param to schema

3f73e33

module & subwf updates

787319b

make bwameth cache lenient until the touch index folder issue is reso…

a199bab

…lved

sateeshperi requested a review from a team as a code owner November 30, 2024 08:15

sateeshperi requested a review from FelixKrueger November 30, 2024 08:15

sateeshperi changed the base branch from master to dev November 30, 2024 08:15

nf-core deleted a comment from github-actions bot Nov 30, 2024

sateeshperi added this to the 2.8.0 milestone Nov 30, 2024

sateeshperi self-assigned this Nov 30, 2024

update changelog

f907936

update bwameth snapshots after install

5bf2730

sateeshperi added 15 commits December 2, 2024 05:58

CI: add gpu tag test job

596a697

CI: add gpu tag test job

e03286f

CI: add gpu tag test job

31af189

CI: add gpu tag test job

af77e4a

CI: add gpu tag test job

0712cf0

CI: add gpu tag test job

4990bf4

CI: add gpu tag test job

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CI: add gpu tag test job

63c856f

CI: add gpu tag test job

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CI: add gpu tag test job

4c00080

CI: add gpu tag test job

2d482c7

CI: add gpu tag test job

d571e3c

add bwameth_gpu test

231cbc3

add gpu profile to config

0b2f069

add bwameth gpu test + snap

b26a4aa

mashehu and others added 23 commits December 5, 2024 10:50

try again 2.1.3 explicitly

1134404

try 2.1.4

0f58839

and now reset back to v2

aaa58d1

increase max_shards to 15

ddb99ae

Corrected test labels, GPU tests with latest-everything, corrected en…

ef2cdcb

…v vars and excluded cancelled from confirm-pass

Disabled latest-everything for now

05cb5c9

Bumped nxf min version to 24.10.2

5d8cc4b

update qualimap paths in nftignore

1e77463

remove test folder contents only

336d466

use ubuntu-latest as default runner

18b389c

use ubuntu-latest as default runner

e98c5de

use ubuntu-latest as default runner

231d9d1

use ubuntu-latest as default runner

f8787df

add latest-everything to matrix

57f5756

correct NXF VER for nf-test

c23d1cc

rm latest-everything from matrix

18119ab

use gpu profile in tests config

099fd57

update test gpu configs

e6cd57b

use gpu+docker/singularity profile for nf-test

9703f60

use gpu,docker/singularity profile for nf-test

b73ea64

use gpu,docker/singularity profile for nf-test

32e716f

update changelog

57db3d8

Merge pull request #478 from nf-core/ci-gpu-tests

8c62106

CI: add gpu tag test job

GallVp reviewed Dec 12, 2024

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GallVp reviewed Dec 12, 2024

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GallVp reviewed Dec 12, 2024

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subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf Show resolved Hide resolved

GallVp reviewed Dec 12, 2024

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subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test Show resolved Hide resolved

GallVp approved these changes Dec 12, 2024

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sateeshperi merged commit a68337a into dev Dec 12, 2024
71 checks passed

sateeshperi deleted the fasta-align-dedup-bwameth branch December 12, 2024 03:50

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Fasta align dedup bwameth #475

Fasta align dedup bwameth #475

sateeshperi commented Nov 30, 2024

github-actions bot commented Nov 30, 2024 •

edited

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❔ Tests ignored:

✅ Tests passed:

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sateeshperi commented Nov 30, 2024

Fasta align dedup bwameth #475

Fasta align dedup bwameth #475

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sateeshperi commented Nov 30, 2024

github-actions bot commented Nov 30, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

sateeshperi commented Nov 30, 2024

github-actions bot commented Nov 30, 2024 •

edited

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