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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
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Re-add picard createorreplacereadgroups for MultiVCFanalyzer #930

Closed jfy133 closed 1 year ago

jfy133 commented 1 year ago

I now remember why we had it in the first place :roll_eyes:

PR checklist

github-actions[bot] commented 1 year ago

This PR is against the master branch :x:

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/eager 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 nf-core/eager 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!

jfy133 commented 1 year ago

@meganemichel and @aidaanva please try this branch -r patch-multivcfanalyzer-readgroups on your data both with and without running MultiVCFAnalyzer and check the VCF files look good (without MVA: include multiple samples in the VCF; with MVA: single samples in VCF so compatible with MVA)

github-actions[bot] commented 1 year ago

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 415d05e

+| ✅ 386 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  32 tests had warnings |!
### :heavy_exclamation_mark: Test warnings: * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable not found in `main.nf`: `params.input_paths` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable not found in `main.nf`: `params.enable_conda` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::python=3.9.4`, `3.10.6` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::markdown=3.3.4`, `3.4.1` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::pymdown-extensions=8.2`, `9.7` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::pygments=2.9.0`, `2.13.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::openjdk=8.0.144`, `17.0.3` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::adapterremoval=2.3.2`, `2.3.3` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::picard=2.26.0`, `2.27.4` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::samtools=1.12`, `1.16.1` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::angsd=0.935`, `0.939` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::gatk4=4.2.0.0`, `4.3.0.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::gatk=3.5`, `3.8` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::damageprofiler=0.4.9`, `1.1` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::multiqc=1.13a`, `1.13` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::libiconv=1.16`, `1.17` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::preseq=3.1.2`, `3.2.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::fastp=0.20.1`, `0.23.2` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::pysam=0.16.0`, `0.19.1` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::pandas=1.2.4`, `1.5.1` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::freebayes=1.3.5`, `1.3.6` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::xopen=1.1.0`, `1.6.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::bowtie2=2.4.4`, `2.4.5` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::eigenstratdatabasetools=1.0.2`, `1.1.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::bbmap=38.92`, `39.01` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::bcftools=1.12`, `1.16` available * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `skip_fastqc` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `skip_adapterremoval` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `skip_preseq` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `skip_deduplication` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `skip_damage_calculation` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `skip_qualimap` ### :grey_question: Tests ignored: * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/CONTRIBUTING.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/workflows/linting.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `docs/README.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `assets/multiqc_config.yaml` ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/markdownlint.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/nf-core-eager_logo.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `bin/markdown_to_html.py` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/images/nf-core-eager_logo.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/output.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/usage.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreSchema.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `main.nf` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `environment.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `Dockerfile` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.name` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.show_hidden_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.schema_ignore_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.container` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.name`` began with ``nf-core/`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.file`` ended with ``.svg`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``process.container`` looks correct: ``nfcore/eager:dev`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` ends in ``dev``: ``'2.4.5dev'`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Lines for loading custom profiles found * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.genome` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.input` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.single_end` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.outdir` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.publish_dir_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.awsqueue` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.awsregion` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.awscli` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.validate_params` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.udg_type` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.single_stranded` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.colour_chemistry` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bam` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.snpcapture_bed` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_convertinputbam` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.fasta` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bwa_index` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bt2_index` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.fasta_index` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.seq_dict` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.large_ref` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.save_reference` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.genomes` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.skip_fastqc` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.skip_adapterremoval` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.skip_preseq` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.skip_deduplication` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.skip_damage_calculation` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.skip_qualimap` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.complexity_filter_poly_g` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.complexity_filter_poly_g_min` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.clip_forward_adaptor` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.clip_reverse_adaptor` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.clip_adapters_list` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.clip_readlength` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.clip_min_read_quality` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.min_adap_overlap` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.skip_collapse` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.skip_trim` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.preserve5p` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.mergedonly` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.qualitymax` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_post_ar_trimming` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.post_ar_trim_front` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.post_ar_trim_tail` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.post_ar_trim_front2` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.post_ar_trim_tail2` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.mapper` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bwaalnn` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bwaalnk` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bwaalnl` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bwaalno` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.circularextension` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.circulartarget` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.circularfilter` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bt2_alignmode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bt2_sensitivity` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bt2n` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bt2l` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bt2_trim5` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bt2_trim3` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bt2_maxins` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.hostremoval_input_fastq` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.hostremoval_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_bam_filtering` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bam_mapping_quality_threshold` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bam_filter_minreadlength` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bam_unmapped_type` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.dedupper` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.dedup_all_merged` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.preseq_step_size` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.preseq_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.preseq_bootstrap` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.preseq_maxextrap` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.preseq_cval` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.preseq_terms` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.damageprofiler_length` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.damageprofiler_threshold` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.damageprofiler_yaxis` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_pmdtools` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pmdtools_range` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pmdtools_threshold` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pmdtools_reference_mask` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pmdtools_max_reads` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pmdtools_platypus` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_mapdamage_rescaling` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.rescale_length_5p` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.rescale_length_3p` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_bedtools_coverage` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.anno_file` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_trim_bam` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_clip_double_stranded_half_udg_left` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_clip_double_stranded_half_udg_right` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_clip_double_stranded_none_udg_left` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_clip_double_stranded_none_udg_right` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_clip_single_stranded_half_udg_left` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_clip_single_stranded_half_udg_right` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_clip_single_stranded_none_udg_left` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_clip_single_stranded_none_udg_right` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.bamutils_softclip` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_genotyping` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.genotyping_tool` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.genotyping_source` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_call_conf` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_ploidy` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_downsample` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_dbsnp` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_hc_out_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_hc_emitrefconf` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_ug_genotype_model` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_ug_out_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_ug_keep_realign_bam` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.gatk_ug_defaultbasequalities` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.freebayes_C` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.freebayes_g` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.freebayes_p` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pileupcaller_snpfile` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pileupcaller_bedfile` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pileupcaller_method` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pileupcaller_transitions_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pileupcaller_min_map_quality` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.pileupcaller_min_base_quality` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.angsd_glmodel` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.angsd_glformat` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.angsd_createfasta` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.angsd_fastamethod` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_bcftools_stats` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_vcf2genome` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.vcf2genome_outfile` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.vcf2genome_header` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.vcf2genome_minc` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.vcf2genome_minq` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.vcf2genome_minfreq` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_multivcfanalyzer` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.write_allele_frequencies` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.min_genotype_quality` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.min_base_coverage` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.min_allele_freq_hom` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.min_allele_freq_het` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.additional_vcf_files` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.reference_gff_annotations` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.reference_gff_exclude` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.snp_eff_results` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_mtnucratio` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.mtnucratio_header` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_sexdeterrmine` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.sexdeterrmine_bedfile` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_nuclear_contamination` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.contamination_chrom_name` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_metagenomic_screening` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.metagenomic_complexity_filter` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.metagenomic_complexity_entropy` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.metagenomic_tool` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.database` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.metagenomic_min_support_reads` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.percent_identity` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.malt_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.malt_alignment_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.malt_top_percent` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.malt_min_support_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.malt_min_support_percent` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.malt_max_queries` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.malt_memory_mode` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.malt_sam_output` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.run_maltextract` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_taxon_list` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_ncbifiles` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_filter` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_toppercent` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_destackingoff` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_downsamplingoff` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_duplicateremovaloff` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_matches` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_megansummary` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_percentidentity` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.maltextract_topalignment` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.multiqc_config` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.email` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.email_on_fail` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.max_multiqc_email_size` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.plaintext_email` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.monochrome_logs` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.help` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.tracedir` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.hostnames` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.config_profile_description` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.config_profile_contact` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.config_profile_url` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.max_memory` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.max_cpus` * [params_used](https://nf-co.re/tools-docs/lint_tests/params_used.html) - Config variable found in `main.nf`: `params.max_time` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/config.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/feature_request.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/markdownlint.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/branch.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/nf-core-eager_logo.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `bin/markdown_to_html.py` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/images/nf-core-eager_logo.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreSchema.groovy` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/push_dockerhub_dev.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/push_dockerhub_release.yml` matches the template * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - CI is building the correct docker image: `docker build --no-cache . -t nfcore/eager:dev` * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - CI is pulling the correct docker image: docker pull nfcore/eager:dev * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:dev * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' checks minimum NF version * [actions_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Nextflow minimum version badge matched config. Badge: `20.07.1`, Config: `20.07.1` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README had a bioconda badge * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda environment name was correct (nf-core-eager-2.4.5dev) * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::python=3.9.4` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::markdown=3.3.4` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::pymdown-extensions=8.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::pygments=2.9.0` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::rename=1.601` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::rename=1.601` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::openjdk=8.0.144` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::fastqc=0.11.9` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::fastqc=0.11.9` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::adapterremoval=2.3.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::adapterremovalfixprefix=0.0.5` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::adapterremovalfixprefix=0.0.5` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::bwa=0.7.17` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::bwa=0.7.17` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::picard=2.26.0` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::samtools=1.12` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::dedup=0.12.8` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::dedup=0.12.8` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::angsd=0.935` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::circularmapper=1.93.5` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::circularmapper=1.93.5` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::gatk4=4.2.0.0` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::gatk=3.5` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::qualimap=2.2.2d` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::qualimap=2.2.2d` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::vcf2genome=0.91` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::vcf2genome=0.91` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::damageprofiler=0.4.9` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::multiqc=1.13a` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::pmdtools=0.60` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::pmdtools=0.60` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::bedtools=2.30.0` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::bedtools=2.30.0` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::libiconv=1.16` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::pigz=2.6` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `conda-forge::pigz=2.6` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::sequencetools=1.5.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::sequencetools=1.5.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::preseq=3.1.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::fastp=0.20.1` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::bamutil=1.0.15` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::bamutil=1.0.15` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::mtnucratio=0.7` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::mtnucratio=0.7` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::pysam=0.16.0` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::kraken2=2.1.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::kraken2=2.1.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::pandas=1.2.4` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::freebayes=1.3.5` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::sexdeterrmine=1.1.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::sexdeterrmine=1.1.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::multivcfanalyzer=0.85.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::multivcfanalyzer=0.85.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::hops=0.35` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::hops=0.35` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::biopython=1.79` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `conda-forge::biopython=1.79` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `conda-forge::xopen=1.1.0` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::bowtie2=2.4.4` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::eigenstratdatabasetools=1.0.2` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::mapdamage2=2.2.1` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::mapdamage2=2.2.1` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::bbmap=38.92` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep had pinned version number: `bioconda::bcftools=1.12` * [conda_dockerfile](https://nf-co.re/tools-docs/lint_tests/conda_dockerfile.html) - Found all expected strings in Dockerfile file * [pipeline_name_conventions](https://nf-co.re/tools-docs/lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools-docs/lint_tests/template_strings.html) - Did not find any Jinja template strings (151 files) * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: push_dockerhub_dev.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: push_dockerhub_release.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: awstest.yml * [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - No merge markers found in pipeline files ### Run details * nf-core/tools version 1.14 * Run at `2022-10-24 09:32:23`
TCLamnidis commented 1 year ago

isnt the tool called AddOrReplaceReadGroups?

meganemichel commented 1 year ago

Tested patch and confirm that running with --run_multivcfanalyzer triggers updating of read groups, while running without --run_multivcfanalyzer produces unmodified vcfs.