Try fix for damageprofiler sometimes needing a fai file

[jfy133]

Add fix for damageprofiler edge case requiring FAI file.

PR checklist

• [ ] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • [ ] If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
• [ ] Make sure your code lints (nf-core lint .).
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker).
• [ ] Usage Documentation in docs/usage.md is updated.
• [ ] Output Documentation in docs/output.md is updated.
• [ ] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).

[github-actions[bot]]

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

Posted for pipeline commit 7c848e4

+| ✅ 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`params.enable_conda` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::python=3.9.4`, `3.11.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::markdown=3.3.4`, `3.4.1` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::pymdown-extensions=8.2`, `9.7` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::pygments=2.9.0`, `2.13.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::openjdk=8.0.144`, `17.0.3` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::adapterremoval=2.3.2`, `2.3.3` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: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`, `0.940` 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: `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`, `2.5.0` 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: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 `2022-11-02 11:05:04`

[jfy133]

i have confirmation from @asmaa-a-abdelwahab that this works it seems (at least doesn't get this particular error)