Updating parameters schema and readme

[reganhayward]

Tidied up some of the params in the schema that were linked to the old params.md page
Also removed the params link in the readme.md

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/dualrnaseq 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]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ad445ca

+| ✅ 259 tests passed       |+
!| ❗  20 tests had warnings |!

❗ Test warnings:

• conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
• conda_env_yaml - Conda dep outdated: bioconda::salmon=1.3.0, 1.5.1 available
• conda_env_yaml - Conda dep outdated: bioconda::STAR=2.7.3a, 2.7.9a available
• conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.8, 1.10.1 available
• conda_env_yaml - Conda dep outdated: bioconda::htseq=0.12.4, 0.13.5 available
• conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.87, 38.90 available
• conda_env_yaml - Conda dep outdated: bioconda::cutadapt=3.2, 3.4 available
• conda_env_yaml - Conda dep outdated: bioconda::pysam=0.15.3, 0.16.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-rtracklayer=1.48.0, 1.52.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-tximport=1.16.0, 1.20.0 available
• conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.6, 3.9.5 available
• conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1, 3.3.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0, 8.2 available
• conda_env_yaml - Conda dep outdated: conda-forge::numpy=1.19.5, 1.21.0 available
• conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.1.5, 1.2.5 available
• conda_env_yaml - Conda dep outdated: conda-forge::biopython=1.78, 1.79 available
• conda_env_yaml - Conda dep outdated: conda-forge::seaborn=0.10.0, 0.11.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::matplotlib=3.1.1, 3.4.2 available
• schema_params - Schema param genomes_ignore not found from nextflow config
• schema_description - No description provided in schema for parameter: genomes_ignore

✅ 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-dualrnaseq_logo.png
• files_exist - File found: bin/markdown_to_html.py
• files_exist - File found: docs/images/nf-core-dualrnaseq_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/dualrnaseq:dev
• nextflow_config - Config manifest.version ends in dev: '1.1.0dev'
• 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_host
• params_used - Config variable found in main.nf: params.genome_pathogen
• params_used - Config variable found in main.nf: params.input
• params_used - Config variable found in main.nf: params.input_paths
• 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.run_cutadapt
• params_used - Config variable found in main.nf: params.a
• params_used - Config variable found in main.nf: params.A
• params_used - Config variable found in main.nf: params.quality_cutoff
• params_used - Config variable found in main.nf: params.cutadapt_params
• params_used - Config variable found in main.nf: params.run_bbduk
• params_used - Config variable found in main.nf: params.minlen
• params_used - Config variable found in main.nf: params.qtrim
• params_used - Config variable found in main.nf: params.trimq
• params_used - Config variable found in main.nf: params.ktrim
• params_used - Config variable found in main.nf: params.k
• params_used - Config variable found in main.nf: params.mink
• params_used - Config variable found in main.nf: params.hdist
• params_used - Config variable found in main.nf: params.adapters
• params_used - Config variable found in main.nf: params.bbduk_params
• params_used - Config variable found in main.nf: params.skip_fastqc
• params_used - Config variable found in main.nf: params.fastqc_params
• params_used - Config variable found in main.nf: params.libtype
• params_used - Config variable found in main.nf: params.generate_salmon_uniq_ambig
• params_used - Config variable found in main.nf: params.incompatPrior
• params_used - Config variable found in main.nf: params.gene_attribute_gff_to_create_transcriptome_host
• params_used - Config variable found in main.nf: params.gene_feature_gff_to_create_transcriptome_host
• params_used - Config variable found in main.nf: params.gene_attribute_gff_to_create_transcriptome_pathogen
• params_used - Config variable found in main.nf: params.gene_feature_gff_to_create_transcriptome_pathogen
• params_used - Config variable found in main.nf: params.read_transcriptome_fasta_host_from_file
• params_used - Config variable found in main.nf: params.read_transcriptome_fasta_pathogen_from_file
• params_used - Config variable found in main.nf: params.run_salmon_selective_alignment
• params_used - Config variable found in main.nf: params.kmer_length
• params_used - Config variable found in main.nf: params.writeUnmappedNames
• params_used - Config variable found in main.nf: params.softclipOverhangs
• params_used - Config variable found in main.nf: params.dumpEq
• params_used - Config variable found in main.nf: params.writeMappings
• params_used - Config variable found in main.nf: params.keepDuplicates
• params_used - Config variable found in main.nf: params.salmon_sa_params_index
• params_used - Config variable found in main.nf: params.salmon_sa_params_mapping
• params_used - Config variable found in main.nf: params.run_star
• params_used - Config variable found in main.nf: params.outSAMunmapped
• params_used - Config variable found in main.nf: params.outSAMattributes
• params_used - Config variable found in main.nf: params.outFilterMultimapNmax
• params_used - Config variable found in main.nf: params.outFilterType
• params_used - Config variable found in main.nf: params.alignSJoverhangMin
• params_used - Config variable found in main.nf: params.alignSJDBoverhangMin
• params_used - Config variable found in main.nf: params.outFilterMismatchNmax
• params_used - Config variable found in main.nf: params.outFilterMismatchNoverReadLmax
• params_used - Config variable found in main.nf: params.alignIntronMin
• params_used - Config variable found in main.nf: params.alignIntronMax
• params_used - Config variable found in main.nf: params.alignMatesGapMax
• params_used - Config variable found in main.nf: params.limitBAMsortRAM
• params_used - Config variable found in main.nf: params.winAnchorMultimapNmax
• params_used - Config variable found in main.nf: params.sjdbOverhang
• params_used - Config variable found in main.nf: params.outWigType
• params_used - Config variable found in main.nf: params.outWigStrand
• params_used - Config variable found in main.nf: params.star_index_params
• params_used - Config variable found in main.nf: params.star_alignment_params
• params_used - Config variable found in main.nf: params.quantTranscriptomeBan
• params_used - Config variable found in main.nf: params.star_salmon_index_params
• params_used - Config variable found in main.nf: params.star_salmon_alignment_params
• params_used - Config variable found in main.nf: params.run_salmon_alignment_based_mode
• params_used - Config variable found in main.nf: params.salmon_alignment_based_params
• params_used - Config variable found in main.nf: params.run_htseq_uniquely_mapped
• params_used - Config variable found in main.nf: params.stranded
• params_used - Config variable found in main.nf: params.max_reads_in_buffer
• params_used - Config variable found in main.nf: params.minaqual
• params_used - Config variable found in main.nf: params.gene_feature_gff_to_quantify_host
• params_used - Config variable found in main.nf: params.gene_feature_gff_to_quantify_pathogen
• params_used - Config variable found in main.nf: params.host_gff_attribute
• params_used - Config variable found in main.nf: params.pathogen_gff_attribute
• params_used - Config variable found in main.nf: params.htseq_params
• params_used - Config variable found in main.nf: params.mapping_statistics
• params_used - Config variable found in main.nf: params.rna_classes_to_replace_host
• 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.validate_params
• 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
• params_used - Config variable found in main.nf: params.fasta_host
• params_used - Config variable found in main.nf: params.fasta_pathogen
• params_used - Config variable found in main.nf: params.gff_host_tRNA
• params_used - Config variable found in main.nf: params.gff_host_genome
• params_used - Config variable found in main.nf: params.gff_pathogen
• params_used - Config variable found in main.nf: params.transcriptome_host
• params_used - Config variable found in main.nf: params.transcriptome_pathogen
• 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/CONTRIBUTING.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.md 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 - .github/workflows/linting.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-dualrnaseq_logo.png matches the template
• files_unchanged - bin/markdown_to_html.py matches the template
• files_unchanged - docs/images/nf-core-dualrnaseq_logo.png matches the template
• files_unchanged - docs/README.md 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
• files_unchanged - assets/multiqc_config.yaml 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/dualrnaseq:dev
• actions_ci - CI is pulling the correct docker image: docker pull nfcore/dualrnaseq:dev
• actions_ci - CI is tagging docker image correctly: docker tag nfcore/dualrnaseq:dev nfcore/dualrnaseq: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: 20.10.0, Config: 20.10.0
• readme - README had a bioconda badge
• conda_env_yaml - Conda environment name was correct (nf-core-dualrnaseq-1.1.0dev)
• 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::samtools=1.9
• conda_env_yaml - Conda dep had pinned version number: bioconda::salmon=1.3.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::STAR=2.7.3a
• conda_env_yaml - Conda dep had pinned version number: bioconda::gffread=0.12.1
• conda_env_yaml - Conda package is the latest available: bioconda::gffread=0.12.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.8
• conda_env_yaml - Conda dep had pinned version number: bioconda::htseq=0.12.4
• conda_env_yaml - Conda dep had pinned version number: bioconda::bbmap=38.87
• conda_env_yaml - Conda dep had pinned version number: bioconda::cutadapt=3.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::pysam=0.15.3
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-rtracklayer=1.48.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-tximport=1.16.0
• conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.7.6
• conda_env_yaml - Conda dep had pinned version number: conda-forge::r-plyr=1.8.6
• conda_env_yaml - Conda package is the latest available: conda-forge::r-plyr=1.8.6
• conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.1.1
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=6.0
• conda_env_yaml - Conda dep had pinned version number: conda-forge::numpy=1.19.5
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pandas=1.1.5
• conda_env_yaml - Conda dep had pinned version number: conda-forge::biopython=1.78
• conda_env_yaml - Conda dep had pinned version number: conda-forge::seaborn=0.10.0
• conda_env_yaml - Conda dep had pinned version number: conda-forge::matplotlib=3.1.1
• 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 (112 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• merge_markers - No merge markers found in pipeline files

Run details

• nf-core/tools version 1.14
• Run at 2021-06-24 02:34:08

[ewels]

Speed look on my phone, but I think you could probably make the schema quite a bit more powerful by using enum to limit options. Remember that you can also use pattern to apply regexes to strings too. The more you validate inputs like this, the better..

[ewels]

Please use the enum option in the schema to limit the options that can be entered if there are only specific valid values.

This can be done via the little settings cog on the right hand side in the nf-core schema build GUI.

[ewels]

Is this meant to be a string?