bump version to 1.2.0dev

[KevinMenden]

bump version to 1.2.0dev

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 306b024

+| ✅ 214 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  11 tests had warnings |!

❗ Test warnings:

• conda_env_yaml - Conda dep outdated: conda-forge::r-base=3.6.3, 4.1.0 available
• conda_env_yaml - Conda dep outdated: conda-forge::r-statmod=1.4.32, 1.4.36 available
• conda_env_yaml - Conda dep outdated: conda-forge::r-data.table=1.12.4, 1.14.0 available
• conda_env_yaml - Conda dep outdated: conda-forge::r-gplots=3.0.1.1, 3.1.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::r-r.methodss3=1.7.1, 1.8.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1, 3.3.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0, 8.2 available
• conda_env_yaml - Conda dep outdated: bioconda::seqkit=0.16.0, 0.16.1 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-edger=3.26.5, 3.34.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-limma=3.40.2, 3.48.0 available

❔ Tests ignored:

• files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy

✅ 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-smrnaseq_logo.png
• files_exist - File found: bin/markdown_to_html.py
• files_exist - File found: docs/images/nf-core-smrnaseq_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/smrnaseq:dev
• nextflow_config - Config manifest.version ends in dev: '1.2.0dev'
• 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.input
• params_used - Config variable found in main.nf: params.input_paths
• params_used - Config variable found in main.nf: params.outdir
• params_used - Config variable found in main.nf: params.protocol
• params_used - Config variable found in main.nf: params.genome
• params_used - Config variable found in main.nf: params.mirna_gtf
• params_used - Config variable found in main.nf: params.bt_indices
• params_used - Config variable found in main.nf: params.mirtrace_protocol
• params_used - Config variable found in main.nf: params.references_parsed
• params_used - Config variable found in main.nf: params.mature
• params_used - Config variable found in main.nf: params.hairpin
• params_used - Config variable found in main.nf: params.clip_r1
• params_used - Config variable found in main.nf: params.three_prime_clip_r1
• params_used - Config variable found in main.nf: params.three_prime_adapter
• params_used - Config variable found in main.nf: params.min_length
• params_used - Config variable found in main.nf: params.skip_qc
• params_used - Config variable found in main.nf: params.skip_fastqc
• params_used - Config variable found in main.nf: params.skip_multiqc
• params_used - Config variable found in main.nf: params.skip_mirdeep
• params_used - Config variable found in main.nf: params.save_reference
• params_used - Config variable found in main.nf: params.seq_center
• params_used - Config variable found in main.nf: params.trim_galore_max_length
• 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.publish_dir_mode
• 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.bt_index
• params_used - Config variable found in main.nf: params.mirtrace_species
• params_used - Config variable found in main.nf: params.fasta
• 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-smrnaseq_logo.png matches the template
• files_unchanged - bin/markdown_to_html.py matches the template
• files_unchanged - docs/images/nf-core-smrnaseq_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 - .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/smrnaseq:dev
• actions_ci - CI is pulling the correct docker image: docker pull nfcore/smrnaseq:dev
• actions_ci - CI is tagging docker image correctly: docker tag nfcore/smrnaseq:dev nfcore/smrnaseq: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: 20.04.0, Config: 20.04.0
• readme - README had a bioconda badge
• conda_env_yaml - Conda environment name was correct (nf-core-smrnaseq-1.2.0dev)
• conda_env_yaml - Conda dep had pinned version number: conda-forge::r-base=3.6.3
• conda_env_yaml - Conda dep had pinned version number: conda-forge::r-statmod=1.4.32
• conda_env_yaml - Conda dep had pinned version number: conda-forge::r-data.table=1.12.4
• conda_env_yaml - Conda dep had pinned version number: conda-forge::r-gplots=3.0.1.1
• conda_env_yaml - Conda dep had pinned version number: conda-forge::r-r.methodss3=1.7.1
• conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.7.3
• 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::pygments=2.9.0
• conda_env_yaml - Conda package is the latest available: conda-forge::pygments=2.9.0
• 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::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::trim-galore=0.6.6
• conda_env_yaml - Conda package is the latest available: bioconda::trim-galore=0.6.6
• conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.12
• conda_env_yaml - Conda package is the latest available: bioconda::samtools=1.12
• conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie=1.3.0
• conda_env_yaml - Conda package is the latest available: bioconda::bowtie=1.3.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.10.1
• conda_env_yaml - Conda package is the latest available: bioconda::multiqc=1.10.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::mirtop=0.4.23
• conda_env_yaml - Conda package is the latest available: bioconda::mirtop=0.4.23
• conda_env_yaml - Conda dep had pinned version number: bioconda::seqcluster=1.2.7
• conda_env_yaml - Conda package is the latest available: bioconda::seqcluster=1.2.7
• conda_env_yaml - Conda dep had pinned version number: bioconda::htseq=0.13.5
• conda_env_yaml - Conda package is the latest available: bioconda::htseq=0.13.5
• conda_env_yaml - Conda dep had pinned version number: bioconda::fastx_toolkit=0.0.14
• conda_env_yaml - Conda package is the latest available: bioconda::fastx_toolkit=0.0.14
• conda_env_yaml - Conda dep had pinned version number: bioconda::seqkit=0.16.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::mirtrace=1.0.1
• conda_env_yaml - Conda package is the latest available: bioconda::mirtrace=1.0.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-edger=3.26.5
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-limma=3.40.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::mirdeep2=2.0.1.2
• conda_env_yaml - Conda package is the latest available: bioconda::mirdeep2=2.0.1.2
• 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 (55 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: ci.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• merge_markers - No merge markers found in pipeline files

Run details

• nf-core/tools version 1.14
• Run at 2021-06-15 12:53:20