Master fusionv2.3.5 patch

[schavan13]

replace 'cp' in sortmerna with 'mv'

[github-actions]

nf-core lint overall result: Failed ❌

Posted for pipeline commit 450df62

+| ✅ 201 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌  13 tests failed       |-

❌ Test failures:

• files_exist - File must be removed: lib/NfcoreTemplate.groovy
• files_exist - File must be removed: lib/Utils.groovy
• files_exist - File must be removed: lib/WorkflowMain.groovy
• files_exist - File must be removed: lib/WorkflowRnaseq.groovy
• files_exist - File must be removed: lib/nfcore_external_java_deps.jar
• nextflow_config - Config default value incorrect: params.ribo_database_manifest is set as ${projectDir}/assets/rrna-db-defaults.txt in nextflow_schema.json but is /home/runner/work/nf-core-rnaseq-watchmaker/nf-core-rnaseq-watchmaker/assets/rrna-db-defaults.txt in nextflow.config.
• files_unchanged - .github/CONTRIBUTING.md does not match the template
• files_unchanged - .github/workflows/branch.yml does not match the template
• files_unchanged - .github/workflows/linting_comment.yml does not match the template
• files_unchanged - .github/workflows/linting.yml does not match the template
• files_unchanged - assets/nf-core-rnaseq_logo_light.png does not match the template
• files_unchanged - docs/images/nf-core-rnaseq_logo_light.png does not match the template
• files_unchanged - docs/images/nf-core-rnaseq_logo_dark.png does not match the template

❗ Test warnings:

• files_exist - File not found: .github/workflows/awstest.yml
• files_exist - File not found: .github/workflows/awsfulltest.yml
• nextflow_config - Config manifest.version should end in dev: 3.14.0
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.
• nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

• files_unchanged - File ignored due to lint config: assets/email_template.html
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nf-core-rnaseq-watchmaker/nf-core-rnaseq-watchmaker/.github/workflows/awstest.yml
• multiqc_config - multiqc_config

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.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.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.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-rnaseq_logo_light.png
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/images/nf-core-rnaseq_logo_light.png
• files_exist - File found: docs/images/nf-core-rnaseq_logo_dark.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: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: modules.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• 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: docs/images/nf-core-rnaseq_logo.png
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• 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.validationShowHiddenParams
• nextflow_config - Config variable found: params.validationSchemaIgnoreParams
• 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 (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 variable (correctly) not found: params.enable_conda
• 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 .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• 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
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.hisat2_build_memory= 200.GB
• nextflow_config - Config default value correct: params.gtf_extra_attributes= gene_name
• nextflow_config - Config default value correct: params.gtf_group_features= gene_id
• nextflow_config - Config default value correct: params.featurecounts_group_type= gene_biotype
• nextflow_config - Config default value correct: params.featurecounts_feature_type= exon
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes
• nextflow_config - Config default value correct: params.trimmer= trimgalore
• nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
• nextflow_config - Config default value correct: params.umitools_extract_method= string
• nextflow_config - Config default value correct: params.umitools_grouping_method= directional
• nextflow_config - Config default value correct: params.aligner= star_salmon
• nextflow_config - Config default value correct: params.pseudo_aligner_kmer_size= 31
• nextflow_config - Config default value correct: params.min_mapped_reads= 5.0
• nextflow_config - Config default value correct: params.kallisto_quant_fraglen= 200
• nextflow_config - Config default value correct: params.kallisto_quant_fraglen_sd= 200
• nextflow_config - Config default value correct: params.deseq2_vst= true
• nextflow_config - Config default value correct: params.rseqc_modules= bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
• nextflow_config - Config default value correct: params.skip_bbsplit= true
• nextflow_config - Config default value correct: params.skip_preseq= true
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.test_data_base= https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3
• nextflow_config - Config default value correct: params.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 128.GB
• nextflow_config - Config default value correct: params.max_time= 240.h
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
• nextflow_config - Config default value correct: params.validate_params= true
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml 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/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (273 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: cloud_tests_full.yml
• actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP_ found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_ found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_ found in conf/modules.config and Nextflow scripts.
• modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
• modules_config - HISAT2_EXTRACTSPLICESITES found in conf/modules.config and Nextflow scripts.
• modules_config - SALMON_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - KALLISTO_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - RSEM_PREPAREREFERENCE_GENOME found in conf/modules.config and Nextflow scripts.
• modules_config - GTF2BED found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_ADDITIONAL_FASTA found in conf/modules.config and Nextflow scripts.
• modules_config - GTF_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_GETCHROMSIZES found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
• modules_config - FQ_SUBSAMPLE found in conf/modules.config and Nextflow scripts.
• modules_config - UMITOOLS_EXTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - BBMAP_BBSPLIT found in conf/modules.config and Nextflow scripts.
• modules_config - SORTMERNA found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_GENOMECOV found in conf/modules.config and Nextflow scripts.
• modules_config - STRINGTIE_STRINGTIE found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - DESEQ2_QC_STAR_SALMON found in conf/modules.config and Nextflow scripts.
• modules_config - DESEQ2_QC_RSEM found in conf/modules.config and Nextflow scripts.
• modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
• modules_config - QUALIMAP_RNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - DUPRADAR found in conf/modules.config and Nextflow scripts.
• modules_config - SUBREAD_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC_CUSTOM_BIOTYPE found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - DESEQ2_QC_PSEUDO found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline

Run details

• nf-core/tools version 2.14.1
• Run at 2024-09-18 14:26:06