PR to update optimised params and remove bams after bwamem alignment

[Ales-ibt]

PR to update optimised kmer for sourmash, coverage threshold on bwamem, and remove bams after bwamem alignment. The $USER var was added to codon config avoid writing permission conflicts on workdir.

[github-actions]

This PR is against the master 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 @Ales-ibt,

It looks like this pull-request is has been made against the EBI-Metagenomics/shallowmapping master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the EBI-Metagenomics/shallowmapping 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!

[chrisAta]

Looks really good to me! Just a tiny typo spotted

[KateSakharova]

Looks good!

[mberacochea]

The is one module path / diff missing from the nf-core module sourmash / sketch.

Other than that it looks good to me

[mberacochea]

Thank you @Ales-ibt. It looks good to me 👍

[mberacochea]

The linters are angry, let me know if you need a hand fixing those

[Ales-ibt]

Yes please, I'd like to fix the lining problems and rid of the github-actions message This PR is against the master branch

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 14b92ab

+| ✅ 131 tests passed       |+
#| ❔  40 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: .github/workflows/awstest.yml
• files_exist - File not found: .github/workflows/awsfulltest.yml
• pipeline_todos - TODO string in WorkflowShallowmapping.groovy: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
• pipeline_todos - TODO string in ci.yml.bak: You can customise CI pipeline run tests as required
• nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-shallowmapping_logo_light.png
• files_exist - File is ignored: docs/
• files_exist - File is ignored: docs/output.md
• files_exist - File is ignored: docs/README.md
• files_exist - File is ignored: docs/usage.md
• files_exist - File is ignored: docs/images/nf-core-shallowmapping_logo_dark.png
• files_exist - File is ignored: docs/images/nf-core-shallowmapping_logo_light.png
• files_exist - File is ignored: pyproject.toml
• files_exist - File is ignored: .gitignore
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/*
• files_exist - File is ignored: .github/workflows/branch.yml
• files_exist - File is ignored: .github/CONTRIBUTING.md
• files_exist - File is ignored: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/test.config
• files_exist - File is ignored: conf/test_full.config
• files_exist - File is ignored: .github/workflows/ci.yml
• files_exist - File is ignored: lib/Utils.groovy
• files_exist - File is ignored: lib/WorkflowMain.groovy
• files_exist - File is ignored: lib/NfcoreTemplate.groovy
• files_exist - File is ignored: lib/WorkflowShallowmapping.groovy
• files_exist - File is ignored: lib/nfcore_external_java_deps.jar
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config variable ignored: process.cpus
• nextflow_config - Config variable ignored: process.memory
• nextflow_config - Config variable ignored: process.time
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.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 does not exist: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: assets/nf-core-shallowmapping_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-shallowmapping_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-shallowmapping_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• actions_ci - '.github/workflows/ci.yml' not found
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/shallowmapping/shallowmapping/.github/workflows/awstest.yml

✅ Tests passed:

• files_exist - File found: .gitattributes
• 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/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.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: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• 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-shallowmapping_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/Workflow.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.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: 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 dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 1.0dev
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.outdir= results
• 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
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml 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/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md 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 - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• 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_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (101 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: linting.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: release-announcments.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 '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 - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - FASTP found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - SOURMASH_GATHER found in conf/modules.config and Nextflow scripts.
• modules_config - ALIGN_BWAMEM2 found in conf/modules.config and Nextflow scripts.
• modules_config - POSTPROC_SOURMASHTAXO found in conf/modules.config and Nextflow scripts.
• modules_config - POSTPROC_BWATAXO found in conf/modules.config and Nextflow scripts.
• modules_config - POSTPROC_FUNCTIONSPRED found in conf/modules.config and Nextflow scripts.
• modules_config - DRAM_DISTILL found in conf/modules.config and Nextflow scripts.
• modules_config - KEGG_COMPLETENESS found in conf/modules.config and Nextflow scripts.
• modules_config - KEGG_SPECIES found in conf/modules.config and Nextflow scripts.
• modules_config - POSTPROC_INTEGRATOR found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline

Run details

• nf-core/tools version 2.14.1
• Run at 2024-05-23 13:34:25