Export two ASV relative abundance tables with DADA2 or QIIME2 classification

[d4straub]

I prefer to have two relative abundance tables with taxonomic classifications and sequences, for DADA2 and QIIME2 classifications. Those tables are actually the info that my customers prefer and expect but those are currently only produced for QIIME2 classifications. It is quite tedious to merge those tables manually to satisfy the expectations, so here is the automation.

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fa29921

+| ✅ 136 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: conf/igenomes.config
• readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

✅ Tests passed:

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• nextflow_config - Config timeline.enabled had correct value: true
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• nextflow_config - Config manifest.name began with nf-core/
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• nextflow_config - Config manifest.version ends in dev: '2.1.0dev'
• 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
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• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• 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: 21.04.0, Config: 21.04.0
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (147 files)
• schema_lint - Schema lint passed
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• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
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• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json

Run details

• nf-core/tools version 2.1
• Run at 2021-08-09 09:31:53

[erikrikarddaniel]

Looks fine.

[d4straub]

Thanks!