Fix/sample merge #401

sateeshperi · 2024-05-17T07:59:40Z

No description provided.

github-actions · 2024-05-17T08:01:36Z

`nf-core lint` overall result: Passed ✅

Posted for pipeline commit dbd8b43

+| ✅ 212 tests passed       |+
#| ❔   2 tests were ignored |#

❔ Tests ignored:

files_exist - File is ignored: lib/nfcore_external_java_deps.jar
actions_ci - actions_ci

✅ 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/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: assets/nf-core-methylseq_logo_light.png
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/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: .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 - 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: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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 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: 2.7.0dev
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.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.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
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: 23.04.0, Config: 23.04.0
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 (157 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.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 - 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.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
modules_config - BISMARK_GENOMEPREPARATION found in conf/modules.config and Nextflow scripts.
modules_config - BISMARK_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - BISMARK_DEDUPLICATE found in conf/modules.config and Nextflow scripts.
modules_config - BISMARK_METHYLATIONEXTRACTOR found in conf/modules.config and Nextflow scripts.
modules_config - BISMARK_COVERAGE2CYTOSINE found in conf/modules.config and Nextflow scripts.
modules_config - BISMARK_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - BISMARK_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - BWAMETH_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - BWAMETH_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_ALIGNMENTS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DEDUPLICATED found in conf/modules.config and Nextflow scripts.
modules_config - METHYLDACKEL_MBIAS found in conf/modules.config and Nextflow scripts.
modules_config - METHYLDACKEL_EXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - QUALIMAP_BAMQC found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-05-17 11:32:51

main.nf

sateeshperi added 3 commits May 16, 2024 15:24

fix single multiple fastq branching

21499e8

use validateInputSamplesheet function

d51f106

move getGenomeAttribute to main

dbe0715

maxulysse added 2 commits May 17, 2024 11:44

add test_data to schemaignore to remove warning

4046aa6

remove getGenomeAttribute usage for files not in iGenomes

3256eb9

maxulysse reviewed May 17, 2024

View reviewed changes

main.nf Outdated Show resolved Hide resolved

maxulysse added 3 commits May 17, 2024 13:08

Update main.nf

7fd5db0

Merge branch 'dev' into fix/sample-merge

88a6ca8

no need for that

dbd8b43

maxulysse marked this pull request as ready for review May 17, 2024 11:33

maxulysse requested a review from a team as a code owner May 17, 2024 11:33

maxulysse requested a review from FelixKrueger May 17, 2024 11:33

maxulysse approved these changes May 17, 2024

View reviewed changes

maxulysse merged commit 1b18351 into dev May 17, 2024
32 checks passed

sateeshperi deleted the fix/sample-merge branch May 17, 2024 15:20

sateeshperi linked an issue May 17, 2024 that may be closed by this pull request

Latest template merge completely broke dev branch (on AWS + Fusion) #392

Open

edmundmiller mentioned this pull request May 21, 2024

Write tests for samplesheet sample merging/grouping #402

Open

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Fix/sample merge #401

Fix/sample merge #401

sateeshperi commented May 17, 2024

github-actions bot commented May 17, 2024 •

edited

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❔ Tests ignored:

✅ Tests passed:

Run details

Fix/sample merge #401

Fix/sample merge #401

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sateeshperi commented May 17, 2024

github-actions bot commented May 17, 2024 • edited Loading

nf-core lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

github-actions bot commented May 17, 2024 •

edited

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`nf-core lint` overall result: Passed ✅