⬆️ upgrade markduplicate step

[bunop]

fix issue #77

[github-actions]

nf-core lint overall result: Passed ✅

Posted for pipeline commit c8388ac

+| ✅  46 tests passed       |+
#| ❔  25 tests were ignored |#

❔ Tests ignored:

• files_exist - files_exist
• nextflow_config - nextflow_config
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• files_unchanged - File does not exist: .github/.dockstore.yml
• files_unchanged - File does not exist: .github/CONTRIBUTING.md
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.yml
• files_unchanged - File does not exist: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File does not exist: .github/workflows/branch.yml
• files_unchanged - File does not exist: assets/email_template.html
• files_unchanged - File does not exist: assets/email_template.txt
• files_unchanged - File does not exist: assets/sendmail_template.txt
• files_unchanged - File does not exist: assets/nf-core-nf-resequencing-mem_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-nf-resequencing-mem_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-nf-resequencing-mem_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_ci - actions_ci
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-resequencing-mem/nf-resequencing-mem/.github/workflows/awstest.yml
• actions_awsfulltest - actions_awsfulltest
• pipeline_todos - pipeline_todos
• pipeline_name_conventions - pipeline_name_conventions
• merge_markers - merge_markers
• multiqc_config - multiqc_config

✅ Tests passed:

• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml 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.
• template_strings - Did not find any Jinja template strings (203 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: linting_comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - FREEBAYES_CHUNK found in conf/base.config and Nextflow scripts.
• base_config - PICARD_MARKDUPLICATES found in conf/base.config and Nextflow scripts.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_RMDUP_R1 found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_RMDUP_R2 found in conf/modules.config and Nextflow scripts.
• modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_COVERAGE found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES_SPLITCRAM found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES_CHUNK found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES_CONCAT found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES_TABIX found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_NORM found in conf/modules.config and Nextflow scripts.
• modules_config - TABIX_TABIX found in conf/modules.config and Nextflow scripts.
• modules_config - SNPEFF_DOWNLOAD 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
• 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 2024-07-11 11:29:45