Fix mapdamage and add parameter

[jfy133]

Closes #933
Closes #934

PR checklist

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

[github-actions]

This PR is against the master branch ❌

• 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]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 745b63e

+| ✅ 390 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  31 tests had warnings |!

Details

❗ Test warnings:

• params_used - Config variable not found in main.nf: params.input_paths
• params_used - Config variable not found in main.nf: params.enable_conda
• conda_env_yaml - Conda dep outdated: conda-forge::python=3.9.4, 3.11.0 available
• conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.3.4, 3.4.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=8.2, 9.8 available
• conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.9.0, 2.13.0 available
• conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 17.0.3 available
• conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.2, 2.3.3 available
• conda_env_yaml - Conda dep outdated: bioconda::picard=2.26.0, 2.27.4 available
• conda_env_yaml - Conda dep outdated: bioconda::samtools=1.12, 1.16.1 available
• conda_env_yaml - Conda dep outdated: bioconda::angsd=0.935, 0.940 available
• conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.2.0.0, 4.3.0.0 available
• conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
• conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.16, 1.17 available
• conda_env_yaml - Conda dep outdated: bioconda::preseq=3.1.2, 3.2.0 available
• conda_env_yaml - Conda dep outdated: bioconda::fastp=0.20.1, 0.23.2 available
• conda_env_yaml - Conda dep outdated: bioconda::pysam=0.16.0, 0.19.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.2.4, 1.5.1 available
• conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.5, 1.3.6 available
• conda_env_yaml - Conda dep outdated: conda-forge::xopen=1.1.0, 1.7.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bowtie2=2.4.4, 2.5.0 available
• conda_env_yaml - Conda dep outdated: bioconda::eigenstratdatabasetools=1.0.2, 1.1.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.92, 39.01 available
• conda_env_yaml - Conda dep outdated: bioconda::bcftools=1.12, 1.16 available
• schema_description - No description provided in schema for parameter: skip_fastqc
• schema_description - No description provided in schema for parameter: skip_adapterremoval
• schema_description - No description provided in schema for parameter: skip_preseq
• schema_description - No description provided in schema for parameter: skip_deduplication
• schema_description - No description provided in schema for parameter: skip_damage_calculation
• schema_description - No description provided in schema for parameter: skip_qualimap

❔ Tests ignored:

• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File found: .github/markdownlint.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/ci.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: assets/nf-core-eager_logo.png
• files_exist - File found: bin/markdown_to_html.py
• files_exist - File found: docs/images/nf-core-eager_logo.png
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: lib/nfcore_external_java_deps.jar
• files_exist - File found: lib/NfcoreSchema.groovy
• files_exist - File found: main.nf
• files_exist - File found: environment.yml
• files_exist - File found: Dockerfile
• files_exist - File found: conf/base.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .travis.yml
• nextflow_config - Config variable found: manifest.name
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: manifest.homePage
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: params.show_hidden_params
• nextflow_config - Config variable found: params.schema_ignore_params
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable found: process.container
• nextflow_config - Config variable (correctly) not found: params.version
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config manifest.name began with nf-core/
• nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .svg
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config process.container looks correct: nfcore/eager:dev
• nextflow_config - Config manifest.version ends in dev: '2.4.6dev'
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• params_used - Config variable found in main.nf: params.genome
• params_used - Config variable found in main.nf: params.input
• params_used - Config variable found in main.nf: params.single_end
• params_used - Config variable found in main.nf: params.outdir
• params_used - Config variable found in main.nf: params.publish_dir_mode
• params_used - Config variable found in main.nf: params.awsqueue
• params_used - Config variable found in main.nf: params.awsregion
• params_used - Config variable found in main.nf: params.awscli
• params_used - Config variable found in main.nf: params.validate_params
• params_used - Config variable found in main.nf: params.udg_type
• params_used - Config variable found in main.nf: params.single_stranded
• params_used - Config variable found in main.nf: params.colour_chemistry
• params_used - Config variable found in main.nf: params.bam
• params_used - Config variable found in main.nf: params.snpcapture_bed
• params_used - Config variable found in main.nf: params.run_convertinputbam
• params_used - Config variable found in main.nf: params.fasta
• params_used - Config variable found in main.nf: params.bwa_index
• params_used - Config variable found in main.nf: params.bt2_index
• params_used - Config variable found in main.nf: params.fasta_index
• params_used - Config variable found in main.nf: params.seq_dict
• params_used - Config variable found in main.nf: params.large_ref
• params_used - Config variable found in main.nf: params.save_reference
• params_used - Config variable found in main.nf: params.genomes
• params_used - Config variable found in main.nf: params.skip_fastqc
• params_used - Config variable found in main.nf: params.skip_adapterremoval
• params_used - Config variable found in main.nf: params.skip_preseq
• params_used - Config variable found in main.nf: params.skip_deduplication
• params_used - Config variable found in main.nf: params.skip_damage_calculation
• params_used - Config variable found in main.nf: params.skip_qualimap
• params_used - Config variable found in main.nf: params.complexity_filter_poly_g
• params_used - Config variable found in main.nf: params.complexity_filter_poly_g_min
• params_used - Config variable found in main.nf: params.clip_forward_adaptor
• params_used - Config variable found in main.nf: params.clip_reverse_adaptor
• params_used - Config variable found in main.nf: params.clip_adapters_list
• params_used - Config variable found in main.nf: params.clip_readlength
• params_used - Config variable found in main.nf: params.clip_min_read_quality
• params_used - Config variable found in main.nf: params.min_adap_overlap
• params_used - Config variable found in main.nf: params.skip_collapse
• params_used - Config variable found in main.nf: params.skip_trim
• params_used - Config variable found in main.nf: params.preserve5p
• params_used - Config variable found in main.nf: params.mergedonly
• params_used - Config variable found in main.nf: params.qualitymax
• params_used - Config variable found in main.nf: params.run_post_ar_trimming
• params_used - Config variable found in main.nf: params.post_ar_trim_front
• params_used - Config variable found in main.nf: params.post_ar_trim_tail
• params_used - Config variable found in main.nf: params.post_ar_trim_front2
• params_used - Config variable found in main.nf: params.post_ar_trim_tail2
• params_used - Config variable found in main.nf: params.mapper
• params_used - Config variable found in main.nf: params.bwaalnn
• params_used - Config variable found in main.nf: params.bwaalnk
• params_used - Config variable found in main.nf: params.bwaalnl
• params_used - Config variable found in main.nf: params.bwaalno
• params_used - Config variable found in main.nf: params.circularextension
• params_used - Config variable found in main.nf: params.circulartarget
• params_used - Config variable found in main.nf: params.circularfilter
• params_used - Config variable found in main.nf: params.bt2_alignmode
• params_used - Config variable found in main.nf: params.bt2_sensitivity
• params_used - Config variable found in main.nf: params.bt2n
• params_used - Config variable found in main.nf: params.bt2l
• params_used - Config variable found in main.nf: params.bt2_trim5
• params_used - Config variable found in main.nf: params.bt2_trim3
• params_used - Config variable found in main.nf: params.bt2_maxins
• params_used - Config variable found in main.nf: params.hostremoval_input_fastq
• params_used - Config variable found in main.nf: params.hostremoval_mode
• params_used - Config variable found in main.nf: params.run_bam_filtering
• params_used - Config variable found in main.nf: params.bam_mapping_quality_threshold
• params_used - Config variable found in main.nf: params.bam_filter_minreadlength
• params_used - Config variable found in main.nf: params.bam_unmapped_type
• params_used - Config variable found in main.nf: params.dedupper
• params_used - Config variable found in main.nf: params.dedup_all_merged
• params_used - Config variable found in main.nf: params.preseq_step_size
• params_used - Config variable found in main.nf: params.preseq_mode
• params_used - Config variable found in main.nf: params.preseq_bootstrap
• params_used - Config variable found in main.nf: params.preseq_maxextrap
• params_used - Config variable found in main.nf: params.preseq_cval
• params_used - Config variable found in main.nf: params.preseq_terms
• params_used - Config variable found in main.nf: params.damageprofiler_length
• params_used - Config variable found in main.nf: params.damageprofiler_threshold
• params_used - Config variable found in main.nf: params.damageprofiler_yaxis
• params_used - Config variable found in main.nf: params.run_pmdtools
• params_used - Config variable found in main.nf: params.pmdtools_range
• params_used - Config variable found in main.nf: params.pmdtools_threshold
• params_used - Config variable found in main.nf: params.pmdtools_reference_mask
• params_used - Config variable found in main.nf: params.pmdtools_max_reads
• params_used - Config variable found in main.nf: params.pmdtools_platypus
• params_used - Config variable found in main.nf: params.run_mapdamage_rescaling
• params_used - Config variable found in main.nf: params.rescale_length_5p
• params_used - Config variable found in main.nf: params.rescale_length_3p
• params_used - Config variable found in main.nf: params.rescale_seqlength
• params_used - Config variable found in main.nf: params.run_bedtools_coverage
• params_used - Config variable found in main.nf: params.anno_file
• params_used - Config variable found in main.nf: params.run_trim_bam
• params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_half_udg_left
• params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_half_udg_right
• params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_none_udg_left
• params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_none_udg_right
• params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_half_udg_left
• params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_half_udg_right
• params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_none_udg_left
• params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_none_udg_right
• params_used - Config variable found in main.nf: params.bamutils_softclip
• params_used - Config variable found in main.nf: params.run_genotyping
• params_used - Config variable found in main.nf: params.genotyping_tool
• params_used - Config variable found in main.nf: params.genotyping_source
• params_used - Config variable found in main.nf: params.gatk_call_conf
• params_used - Config variable found in main.nf: params.gatk_ploidy
• params_used - Config variable found in main.nf: params.gatk_downsample
• params_used - Config variable found in main.nf: params.gatk_dbsnp
• params_used - Config variable found in main.nf: params.gatk_hc_out_mode
• params_used - Config variable found in main.nf: params.gatk_hc_emitrefconf
• params_used - Config variable found in main.nf: params.gatk_ug_genotype_model
• params_used - Config variable found in main.nf: params.gatk_ug_out_mode
• params_used - Config variable found in main.nf: params.gatk_ug_keep_realign_bam
• params_used - Config variable found in main.nf: params.gatk_ug_defaultbasequalities
• params_used - Config variable found in main.nf: params.freebayes_C
• params_used - Config variable found in main.nf: params.freebayes_g
• params_used - Config variable found in main.nf: params.freebayes_p
• params_used - Config variable found in main.nf: params.pileupcaller_snpfile
• params_used - Config variable found in main.nf: params.pileupcaller_bedfile
• params_used - Config variable found in main.nf: params.pileupcaller_method
• params_used - Config variable found in main.nf: params.pileupcaller_transitions_mode
• params_used - Config variable found in main.nf: params.pileupcaller_min_map_quality
• params_used - Config variable found in main.nf: params.pileupcaller_min_base_quality
• params_used - Config variable found in main.nf: params.angsd_glmodel
• params_used - Config variable found in main.nf: params.angsd_glformat
• params_used - Config variable found in main.nf: params.angsd_createfasta
• params_used - Config variable found in main.nf: params.angsd_fastamethod
• params_used - Config variable found in main.nf: params.run_bcftools_stats
• params_used - Config variable found in main.nf: params.run_vcf2genome
• params_used - Config variable found in main.nf: params.vcf2genome_outfile
• params_used - Config variable found in main.nf: params.vcf2genome_header
• params_used - Config variable found in main.nf: params.vcf2genome_minc
• params_used - Config variable found in main.nf: params.vcf2genome_minq
• params_used - Config variable found in main.nf: params.vcf2genome_minfreq
• params_used - Config variable found in main.nf: params.run_multivcfanalyzer
• params_used - Config variable found in main.nf: params.write_allele_frequencies
• params_used - Config variable found in main.nf: params.min_genotype_quality
• params_used - Config variable found in main.nf: params.min_base_coverage
• params_used - Config variable found in main.nf: params.min_allele_freq_hom
• params_used - Config variable found in main.nf: params.min_allele_freq_het
• params_used - Config variable found in main.nf: params.additional_vcf_files
• params_used - Config variable found in main.nf: params.reference_gff_annotations
• params_used - Config variable found in main.nf: params.reference_gff_exclude
• params_used - Config variable found in main.nf: params.snp_eff_results
• params_used - Config variable found in main.nf: params.run_mtnucratio
• params_used - Config variable found in main.nf: params.mtnucratio_header
• params_used - Config variable found in main.nf: params.run_sexdeterrmine
• params_used - Config variable found in main.nf: params.sexdeterrmine_bedfile
• params_used - Config variable found in main.nf: params.run_nuclear_contamination
• params_used - Config variable found in main.nf: params.contamination_chrom_name
• params_used - Config variable found in main.nf: params.run_metagenomic_screening
• params_used - Config variable found in main.nf: params.metagenomic_complexity_filter
• params_used - Config variable found in main.nf: params.metagenomic_complexity_entropy
• params_used - Config variable found in main.nf: params.metagenomic_tool
• params_used - Config variable found in main.nf: params.database
• params_used - Config variable found in main.nf: params.metagenomic_min_support_reads
• params_used - Config variable found in main.nf: params.percent_identity
• params_used - Config variable found in main.nf: params.malt_mode
• params_used - Config variable found in main.nf: params.malt_alignment_mode
• params_used - Config variable found in main.nf: params.malt_top_percent
• params_used - Config variable found in main.nf: params.malt_min_support_mode
• params_used - Config variable found in main.nf: params.malt_min_support_percent
• params_used - Config variable found in main.nf: params.malt_max_queries
• params_used - Config variable found in main.nf: params.malt_memory_mode
• params_used - Config variable found in main.nf: params.malt_sam_output
• params_used - Config variable found in main.nf: params.run_maltextract
• params_used - Config variable found in main.nf: params.maltextract_taxon_list
• params_used - Config variable found in main.nf: params.maltextract_ncbifiles
• params_used - Config variable found in main.nf: params.maltextract_filter
• params_used - Config variable found in main.nf: params.maltextract_toppercent
• params_used - Config variable found in main.nf: params.maltextract_destackingoff
• params_used - Config variable found in main.nf: params.maltextract_downsamplingoff
• params_used - Config variable found in main.nf: params.maltextract_duplicateremovaloff
• params_used - Config variable found in main.nf: params.maltextract_matches
• params_used - Config variable found in main.nf: params.maltextract_megansummary
• params_used - Config variable found in main.nf: params.maltextract_percentidentity
• params_used - Config variable found in main.nf: params.maltextract_topalignment
• params_used - Config variable found in main.nf: params.multiqc_config
• params_used - Config variable found in main.nf: params.email
• params_used - Config variable found in main.nf: params.email_on_fail
• params_used - Config variable found in main.nf: params.max_multiqc_email_size
• params_used - Config variable found in main.nf: params.plaintext_email
• params_used - Config variable found in main.nf: params.monochrome_logs
• params_used - Config variable found in main.nf: params.help
• params_used - Config variable found in main.nf: params.tracedir
• params_used - Config variable found in main.nf: params.hostnames
• params_used - Config variable found in main.nf: params.config_profile_description
• params_used - Config variable found in main.nf: params.config_profile_contact
• params_used - Config variable found in main.nf: params.config_profile_url
• params_used - Config variable found in main.nf: params.max_memory
• params_used - Config variable found in main.nf: params.max_cpus
• params_used - Config variable found in main.nf: params.max_time
• files_unchanged - .gitattributes matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
• files_unchanged - .github/markdownlint.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - assets/nf-core-eager_logo.png matches the template
• files_unchanged - bin/markdown_to_html.py matches the template
• files_unchanged - docs/images/nf-core-eager_logo.png matches the template
• files_unchanged - lib/nfcore_external_java_deps.jar matches the template
• files_unchanged - lib/NfcoreSchema.groovy matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .github/workflows/push_dockerhub_dev.yml matches the template
• files_unchanged - .github/workflows/push_dockerhub_release.yml matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - CI is building the correct docker image: docker build --no-cache . -t nfcore/eager:dev
• actions_ci - CI is pulling the correct docker image: docker pull nfcore/eager:dev
• actions_ci - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:dev
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
• readme - README Nextflow minimum version badge matched config. Badge: 20.07.1, Config: 20.07.1
• readme - README had a bioconda badge
• conda_env_yaml - Conda environment name was correct (nf-core-eager-2.4.6dev)
• conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.9.4
• conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.3.4
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=8.2
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.9.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::rename=1.601
• conda_env_yaml - Conda package is the latest available: bioconda::rename=1.601
• conda_env_yaml - Conda dep had pinned version number: conda-forge::openjdk=8.0.144
• conda_env_yaml - Conda dep had pinned version number: bioconda::fastqc=0.11.9
• conda_env_yaml - Conda package is the latest available: bioconda::fastqc=0.11.9
• conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremoval=2.3.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremovalfixprefix=0.0.5
• conda_env_yaml - Conda package is the latest available: bioconda::adapterremovalfixprefix=0.0.5
• conda_env_yaml - Conda dep had pinned version number: bioconda::bwa=0.7.17
• conda_env_yaml - Conda package is the latest available: bioconda::bwa=0.7.17
• conda_env_yaml - Conda dep had pinned version number: bioconda::picard=2.26.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.12
• conda_env_yaml - Conda dep had pinned version number: bioconda::dedup=0.12.8
• conda_env_yaml - Conda package is the latest available: bioconda::dedup=0.12.8
• conda_env_yaml - Conda dep had pinned version number: bioconda::angsd=0.935
• conda_env_yaml - Conda dep had pinned version number: bioconda::circularmapper=1.93.5
• conda_env_yaml - Conda package is the latest available: bioconda::circularmapper=1.93.5
• conda_env_yaml - Conda dep had pinned version number: bioconda::gatk4=4.2.0.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::gatk=3.5
• conda_env_yaml - Conda dep had pinned version number: bioconda::qualimap=2.2.2d
• conda_env_yaml - Conda package is the latest available: bioconda::qualimap=2.2.2d
• conda_env_yaml - Conda dep had pinned version number: bioconda::vcf2genome=0.91
• conda_env_yaml - Conda package is the latest available: bioconda::vcf2genome=0.91
• conda_env_yaml - Conda dep had pinned version number: bioconda::damageprofiler=0.4.9
• conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.13
• conda_env_yaml - Conda package is the latest available: bioconda::multiqc=1.13
• conda_env_yaml - Conda dep had pinned version number: bioconda::pmdtools=0.60
• conda_env_yaml - Conda package is the latest available: bioconda::pmdtools=0.60
• conda_env_yaml - Conda dep had pinned version number: bioconda::bedtools=2.30.0
• conda_env_yaml - Conda package is the latest available: bioconda::bedtools=2.30.0
• conda_env_yaml - Conda dep had pinned version number: conda-forge::libiconv=1.16
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pigz=2.6
• conda_env_yaml - Conda package is the latest available: conda-forge::pigz=2.6
• conda_env_yaml - Conda dep had pinned version number: bioconda::sequencetools=1.5.2
• conda_env_yaml - Conda package is the latest available: bioconda::sequencetools=1.5.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::preseq=3.1.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::fastp=0.20.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::bamutil=1.0.15
• conda_env_yaml - Conda package is the latest available: bioconda::bamutil=1.0.15
• conda_env_yaml - Conda dep had pinned version number: bioconda::mtnucratio=0.7
• conda_env_yaml - Conda package is the latest available: bioconda::mtnucratio=0.7
• conda_env_yaml - Conda dep had pinned version number: bioconda::pysam=0.16.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::kraken2=2.1.2
• conda_env_yaml - Conda package is the latest available: bioconda::kraken2=2.1.2
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pandas=1.2.4
• conda_env_yaml - Conda dep had pinned version number: bioconda::freebayes=1.3.5
• conda_env_yaml - Conda dep had pinned version number: bioconda::sexdeterrmine=1.1.2
• conda_env_yaml - Conda package is the latest available: bioconda::sexdeterrmine=1.1.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::multivcfanalyzer=0.85.2
• conda_env_yaml - Conda package is the latest available: bioconda::multivcfanalyzer=0.85.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::hops=0.35
• conda_env_yaml - Conda package is the latest available: bioconda::hops=0.35
• conda_env_yaml - Conda dep had pinned version number: bioconda::malt=0.61
• conda_env_yaml - Conda package is the latest available: bioconda::malt=0.61
• conda_env_yaml - Conda dep had pinned version number: conda-forge::biopython=1.79
• conda_env_yaml - Conda package is the latest available: conda-forge::biopython=1.79
• conda_env_yaml - Conda dep had pinned version number: conda-forge::xopen=1.1.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.4.4
• conda_env_yaml - Conda dep had pinned version number: bioconda::eigenstratdatabasetools=1.0.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::mapdamage2=2.2.1
• conda_env_yaml - Conda package is the latest available: bioconda::mapdamage2=2.2.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::bbmap=38.92
• conda_env_yaml - Conda dep had pinned version number: bioconda::bcftools=1.12
• conda_dockerfile - Found all expected strings in Dockerfile file
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (151 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• merge_markers - No merge markers found in pipeline files

Run details

• nf-core/tools version 1.14
• Run at 2022-11-11 14:25:23

[TCLamnidis]

LGTM

[github-actions]

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:

• Install markdownlint-cli
  • On Mac: brew install markdownlint-cli
  • Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
• Fix the markdown errors
  • Automatically: markdownlint . --config .github/markdownlint.yml --fix
  • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

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