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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
134 stars 79 forks source link

Fix mapdamage and add parameter #935

Closed jfy133 closed 1 year ago

jfy133 commented 1 year ago

Closes #933 Closes #934

PR checklist

github-actions[bot] commented 1 year ago

This PR is against the master branch :x:

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/eager master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the nf-core/eager dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions[bot] commented 1 year ago

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

Posted for pipeline commit 745b63e

+| ✅ 390 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  31 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`params.enable_conda` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::python=3.9.4`, `3.11.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::markdown=3.3.4`, `3.4.1` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::pymdown-extensions=8.2`, `9.8` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::pygments=2.9.0`, `2.13.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::openjdk=8.0.144`, `17.0.3` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `bioconda::adapterremoval=2.3.2`, `2.3.3` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: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:dev`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` ends in ``dev``: ``'2.4.6dev'`` * [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: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-2.4.6dev) * [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 `2022-11-11 14:25:23`
github-actions[bot] commented 1 year ago

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

Once you push these changes the test should pass, and you can hide this comment :+1:

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!