Patch: increase mean/median X coverage significance values

[jfy133]

and improves snp_capture bed coverage

Closes #834

PR checklist

• [x] 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 .).
• [x] 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.
• [x] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).

[github-actions[bot]]

This PR is against the master branch :x:

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

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]]

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

Posted for pipeline commit d90edc3

+| ✅ 389 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`params.enable_conda` * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::python=3.9.4`, `3.11.0` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: `conda-forge::markdown=3.3.4`, `3.4.1` available * [conda_env_yaml](https://nf-co.re/tools-docs/lint_tests/conda_env_yaml.html) - Conda dep outdated: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) - 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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) - 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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) - 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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=1.13` * [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 08:46:21`

[jfy133]