Switch to use standard nf-core iGenomes config

[ewels]

• Replaced genomes.config file with the standard nf-core igenomes.config and updated the documentation.
• Removed the boolean flag params --read_transcriptome_fasta_host_from_file and --read_transcriptome_fasta_pathogen_from_file. These are not needed, as the --transcriptome_host and --transcriptome_pathogen parameters already act as boolean flags if not specified by the user.

PR checklist

• This comment contains a description of changes (with reason).
• 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 ac024c6

+| ✅ 258 tests passed       |+
!| ❗  18 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• conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
• conda_env_yaml - Conda dep outdated: bioconda::salmon=1.3.0, 1.5.1 available
• conda_env_yaml - Conda dep outdated: bioconda::STAR=2.7.3a, 2.7.9a available
• conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.8, 1.10.1 available
• conda_env_yaml - Conda dep outdated: bioconda::htseq=0.12.4, 0.13.5 available
• conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.87, 38.90 available
• conda_env_yaml - Conda dep outdated: bioconda::cutadapt=3.2, 3.4 available
• conda_env_yaml - Conda dep outdated: bioconda::pysam=0.15.3, 0.16.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-rtracklayer=1.48.0, 1.52.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-tximport=1.16.0, 1.20.0 available
• conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.6, 3.9.5 available
• conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1, 3.3.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0, 8.2 available
• conda_env_yaml - Conda dep outdated: conda-forge::numpy=1.19.5, 1.20.3 available
• conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.1.5, 1.2.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::biopython=1.78, 1.79 available
• conda_env_yaml - Conda dep outdated: conda-forge::seaborn=0.10.0, 0.11.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::matplotlib=3.1.1, 3.4.2 available

✅ 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.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
• schema_params - Schema matched params returned from nextflow config
• 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 2021-06-22 07:39:39