Changed endors.py license from GPL to MIT (♥ to @aidaanva for fixing)
Removed erroneous R2 in single-end example in input TSV of usage docs (♥ to @aidaanva for fixing)
https://github.com/nf-core/eager/issues/928 Fixed read group incompatibility by re-adding picard AddOrReplaceReadGroups for MultiVCFAnalyzer (♥ to @aidaanva, @meganemichel for reporting)
Fixed edge case of DamageProfiler occasionally requiring FASTA index (♥ to @asmaa-a-abdelwahab for reporting)
https://github.com/nf-core/eager/issues/834 Increased significance values in general stats table for Qualimap mean/median coverages (♥ to @neija2611 for reporting)
Fixed parameter documentation for --snpcapture_bed regarding on-target SNP stats to state these stats currently not displayed in MultiQC only in the Qualimap results (♥ to @meganemichel and @TCLamnidis for reporting)
https://github.com/nf-core/eager/issues/934 Fixed broken parameter setting in mapDamage2 rescale length (♥ to @ashildv for reporting)
Dependencies
Updated MultiQC to official 1.13 version (rather than alpha)
Added pinned MALT dependency to ensure working version in future versions of eager
Deprecated
PR checklist
[x] This comment contains a description of changes (with reason).
[x] If you've fixed a bug or added code that should be tested, add tests!
[x] Make sure your code lints (nf-core lint .).
[x] Ensure the test suite passes (nextflow run . -profile test,docker).
[x] Usage Documentation in docs/usage.md is updated.
[x] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).
+| ✅ 389 tests passed |+
#| ❔ 5 tests were ignored |#
!| ❗ 32 tests had warnings |!
### :heavy_exclamation_mark: Test warnings:
* [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'2.4.6'``
* [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* [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::python=3.9.4`, `3.11.0` available
* [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::markdown=3.3.4`, `3.4.1` available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`, `9.8` 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`, `0.940` 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: `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`, `1.7.0` available
* [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::bowtie2=2.4.4`, `2.5.0` 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:2.4.6``
* [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.rescale_seqlength`
* [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:2.4.6`
* [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:2.4.6
* [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-2.4.6)
* [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=1.13`
* [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::multiqc=1.13`
* [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: `bioconda::malt=0.61`
* [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda package is the latest available: `bioconda::malt=0.61`
* [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 `2022-11-15 12:32:04`
[2.4.6] - 2022-11-14
Added
Fixed
Dependencies
Deprecated
PR checklist
nf-core lint .
).nextflow run . -profile test,docker
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).