Add nf-test by jfy133 · Pull Request #1063 · nf-core/eager

jfy133 · 2024-04-26T08:57:10Z

… test profile

Initial set up, testing command nf-test test --tag test --profile test,docker

PR checklist

… test profile

github-actions · 2024-04-26T08:59:12Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 43c6bba

+| ✅ 405 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  46 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in ro-crate-metadata.json: "description": "
\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-eager_logo_dark.png">\n <img alt="nf-core/eager" src="docs/images/nf-core-eager_logo_light.png">\n \n
\n\n\n \n\n\n\n\n\n\n\n\n \n\n## Introduction\n\nnf-core/eager is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/eager \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/eager was originally written by The nf-core/eager community.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #eager channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/eager for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
pipeline_todos - TODO string in test_minimal.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test_minimal.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
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
local_component_structure - build_intervals.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - samtools_view_genome.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - filter_bam_fragment_length.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - collect_genotypes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - host_removal.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - print_contamination_angsd.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - circularmapper.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - reference_indexing_single.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - estimate_contamination.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - preprocessing_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - manipulate_damage.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - map.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - genotype.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - metagenomics_postprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - bamfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - merge_libraries.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - preprocessing_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - metagenomics_profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - merge_lanes_inputbam.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - metagenomics_complexityfilter.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - deduplicate.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - run_sex_determination.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - elongate_reference.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - metagenomics.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - reference_indexing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - reference_indexing_multi.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - calculate_damage.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

nextflow_config - Config default ignored: params.contamination_estimation_angsd_hapmap

✅ 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-eager_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-eager_logo_light.png
files_exist - File found: docs/images/nf-core-eager_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: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.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
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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-eager_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/NfcoreTemplate.groovy
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files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowEager.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: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
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: validation.help.enabled
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: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 manifest.version ends in dev: 3.0.0dev
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.fasta_circularmapper_elongationfactor= 500
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.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
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nextflow_config - Config default value correct: params.sequencing_qc_tool= fastqc
nextflow_config - Config default value correct: params.preprocessing_tool= fastp
nextflow_config - Config default value correct: params.preprocessing_minlength= 25
nextflow_config - Config default value correct: params.preprocessing_trim5p= 0
nextflow_config - Config default value correct: params.preprocessing_trim3p= 0
nextflow_config - Config default value correct: params.preprocessing_fastp_complexityfilter_threshold= 10
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_trimbasequalitymin= 20
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_adapteroverlap= 1
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_qualitymax= 41
nextflow_config - Config default value correct: params.fastq_shard_size= 1000000
nextflow_config - Config default value correct: params.mapping_tool= bwaaln
nextflow_config - Config default value correct: params.mapping_bwaaln_n= 0.01
nextflow_config - Config default value correct: params.mapping_bwaaln_k= 2
nextflow_config - Config default value correct: params.mapping_bwaaln_l= 1024
nextflow_config - Config default value correct: params.mapping_bwaaln_o= 2
nextflow_config - Config default value correct: params.mapping_bwamem_k= 19
nextflow_config - Config default value correct: params.mapping_bwamem_r= 1.5
nextflow_config - Config default value correct: params.mapping_bowtie2_alignmode= local
nextflow_config - Config default value correct: params.mapping_bowtie2_sensitivity= sensitive
nextflow_config - Config default value correct: params.mapping_bowtie2_n= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_l= 20
nextflow_config - Config default value correct: params.mapping_bowtie2_trim5= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_trim3= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_maxins= 500
nextflow_config - Config default value correct: params.mapping_mapad_p= 0.03
nextflow_config - Config default value correct: params.mapping_mapad_f= 0.5
nextflow_config - Config default value correct: params.mapping_mapad_t= 0.5
nextflow_config - Config default value correct: params.mapping_mapad_d= 0.02
nextflow_config - Config default value correct: params.mapping_mapad_s= 1.0
nextflow_config - Config default value correct: params.mapping_mapad_i= 0.001
nextflow_config - Config default value correct: params.mapping_mapad_x= 0.5
nextflow_config - Config default value correct: params.mapping_mapad_gapreadenddistance= 5.0
nextflow_config - Config default value correct: params.mapping_mapad_maxnumopengaps= 2.0
nextflow_config - Config default value correct: params.mapping_mapad_baseerrorrate= 0.02
nextflow_config - Config default value correct: params.bamfiltering_minreadlength= 0
nextflow_config - Config default value correct: params.bamfiltering_mappingquality= 0
nextflow_config - Config default value correct: params.bamfiltering_genomicbamfilterflag= 4
nextflow_config - Config default value correct: params.metagenomics_input= unmapped
nextflow_config - Config default value correct: params.metagenomics_complexity_tool= bbduk
nextflow_config - Config default value correct: params.metagenomics_complexity_entropy= 0.3
nextflow_config - Config default value correct: params.metagenomics_prinseq_mode= entropy
nextflow_config - Config default value correct: params.metagenomics_prinseq_dustscore= 0.5
nextflow_config - Config default value correct: params.metagenomics_krakenuniq_ramchunksize= 16G
nextflow_config - Config default value correct: params.metagenomics_malt_mode= BlastN
nextflow_config - Config default value correct: params.metagenomics_malt_alignmentmode= SemiGlobal
nextflow_config - Config default value correct: params.metagenomics_malt_minpercentidentity= 85
nextflow_config - Config default value correct: params.metagenomics_malt_toppercent= 1
nextflow_config - Config default value correct: params.metagenomics_malt_minsupportmode= percent
nextflow_config - Config default value correct: params.metagenomics_malt_minsupportpercent= 0.01
nextflow_config - Config default value correct: params.metagenomics_malt_minsupportreads= 1
nextflow_config - Config default value correct: params.metagenomics_malt_maxqueries= 100
nextflow_config - Config default value correct: params.metagenomics_malt_memorymode= load
nextflow_config - Config default value correct: params.metagenomics_malt_group_size= 0
nextflow_config - Config default value correct: params.metagenomics_maltextract_filter= def_anc
nextflow_config - Config default value correct: params.metagenomics_maltextract_toppercent= 0.01
nextflow_config - Config default value correct: params.metagenomics_maltextract_minpercentidentity= 85.0
nextflow_config - Config default value correct: params.deduplication_tool= markduplicates
nextflow_config - Config default value correct: params.damage_manipulation_rescale_seqlength= 12
nextflow_config - Config default value correct: params.damage_manipulation_rescale_length_5p= 0
nextflow_config - Config default value correct: params.damage_manipulation_rescale_length_3p= 0
nextflow_config - Config default value correct: params.damage_manipulation_pmdtools_threshold= 3
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_none_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_none_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_half_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_half_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_none_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_none_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_half_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_half_udg_right= 0
nextflow_config - Config default value correct: params.genotyping_reference_ploidy= 2
nextflow_config - Config default value correct: params.genotyping_pileupcaller_min_base_quality= 30
nextflow_config - Config default value correct: params.genotyping_pileupcaller_min_map_quality= 30
nextflow_config - Config default value correct: params.genotyping_pileupcaller_method= randomHaploid
nextflow_config - Config default value correct: params.genotyping_pileupcaller_transitions_mode= AllSites
nextflow_config - Config default value correct: params.genotyping_gatk_call_conf= 30
nextflow_config - Config default value correct: params.genotyping_gatk_ug_downsample= 250
nextflow_config - Config default value correct: params.genotyping_gatk_ug_out_mode= EMIT_VARIANTS_ONLY
nextflow_config - Config default value correct: params.genotyping_gatk_ug_genotype_mode= SNP
nextflow_config - Config default value correct: params.genotyping_gatk_ug_defaultbasequalities= -1
nextflow_config - Config default value correct: params.genotyping_gatk_hc_out_mode= EMIT_VARIANTS_ONLY
nextflow_config - Config default value correct: params.genotyping_gatk_hc_emitrefconf= GVCF
nextflow_config - Config default value correct: params.genotyping_freebayes_min_alternate_count= 1
nextflow_config - Config default value correct: params.genotyping_freebayes_skip_coverage= 0
nextflow_config - Config default value correct: params.genotyping_angsd_glmodel= samtools
nextflow_config - Config default value correct: params.genotyping_angsd_glformat= binary
nextflow_config - Config default value correct: params.mitochondrion_header= MT
nextflow_config - Config default value correct: params.mapstats_preseq_mode= c_curve
nextflow_config - Config default value correct: params.mapstats_preseq_stepsize= 1000
nextflow_config - Config default value correct: params.mapstats_preseq_terms= 100
nextflow_config - Config default value correct: params.mapstats_preseq_maxextrap= 10000000000
nextflow_config - Config default value correct: params.mapstats_preseq_bootstrap= 100
nextflow_config - Config default value correct: params.mapstats_preseq_cval= 0.95
nextflow_config - Config default value correct: params.damagecalculation_tool= damageprofiler
nextflow_config - Config default value correct: params.damagecalculation_yaxis= 0.3
nextflow_config - Config default value correct: params.damagecalculation_xaxis= 25
nextflow_config - Config default value correct: params.damagecalculation_damageprofiler_length= 100
nextflow_config - Config default value correct: params.damagecalculation_mapdamage_downsample= 0
nextflow_config - Config default value correct: params.host_removal_mode= remove
nextflow_config - Config default value correct: params.contamination_estimation_angsd_chrom_name= X
nextflow_config - Config default value correct: params.contamination_estimation_angsd_range_from= 5000000
nextflow_config - Config default value correct: params.contamination_estimation_angsd_range_to= 154900000
nextflow_config - Config default value correct: params.contamination_estimation_angsd_mapq= 30
nextflow_config - Config default value correct: params.contamination_estimation_angsd_minq= 30
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/CONTRIBUTING.md 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 - .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-eager_logo_light.png matches the template
files_unchanged - docs/images/nf-core-eager_logo_light.png matches the template
files_unchanged - docs/images/nf-core-eager_logo_dark.png 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
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: 24.04.2, Config: 24.04.2
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 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: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_CONVERT_BAM_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ_CONVERTED_BAM found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_PROCESSED found in conf/modules.config and Nextflow scripts.
modules_config - FALCO found in conf/modules.config and Nextflow scripts.
modules_config - FALCO_PROCESSED found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_PAIRED found in conf/modules.config and Nextflow scripts.
modules_config - ADAPTERREMOVAL_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - ADAPTERREMOVAL_PAIRED found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ_ADAPTERREMOVAL found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_PMDFASTA found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_CREATESEQUENCEDICTIONARY found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_ELONGATED_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - CIRCULARMAPPER_CIRCULARGENERATOR found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX_CIRCULARISED found in conf/modules.config and Nextflow scripts.
modules_config - MAPAD_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_BAM_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_MERGED_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_MERGED_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_MERGED_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_BAM_FRAGMENT_LENGTH found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_BAM_FILTERING found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_LENGTH_FILTER_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ_SAVEBAMFILTERINGREADS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ_METAGENOMICS found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ_METAGENOMICS found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SPLIT2 found in conf/modules.config and Nextflow scripts.
modules_config - BWA_ALN found in conf/modules.config and Nextflow scripts.
modules_config - BWA_SAMSE found in conf/modules.config and Nextflow scripts.
modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_MEM found in conf/modules.config and Nextflow scripts.
modules_config - MAPAD_MAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_MAPAD found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_MEM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE_LANES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_MERGED_LANES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_MERGED_LANES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_MERGED_LANES found in conf/modules.config and Nextflow scripts.
modules_config - CIRCULARMAPPER_REALIGNSAMFILE found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - DEDUP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE_DEDUPPED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_DEDUPPED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DEDUPPED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_DEDUPPED found in conf/modules.config and Nextflow scripts.
modules_config - HOST_REMOVAL found in conf/modules.config and Nextflow scripts.
modules_config - ENDORSPY found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_CCURVE found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_COVERAGE_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_COVERAGE_BREADTH found in conf/modules.config and Nextflow scripts.
modules_config - ANGSD_DOCOUNTS found in conf/modules.config and Nextflow scripts.
modules_config - ANGSD_CONTAMINATION found in conf/modules.config and Nextflow scripts.
modules_config - PRINT_CONTAMINATION_ANGSD found in conf/modules.config and Nextflow scripts.
modules_config - MTNUCRATIO found in conf/modules.config and Nextflow scripts.
modules_config - QUALIMAP_BAMQC_WITHBED found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
modules_config - CAT_CAT_MALT found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
modules_config - MALTEXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - MEGAN_RMA2INFO found in conf/modules.config and Nextflow scripts.
modules_config - AMPS found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
modules_config - DAMAGEPROFILER found in conf/modules.config and Nextflow scripts.
modules_config - CALCULATE_MAPDAMAGE2 found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_DEPTH_SEXDETERRMINE found in conf/modules.config and Nextflow scripts.
modules_config - SEXDETERRMINE found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MASKFASTA found in conf/modules.config and Nextflow scripts.
modules_config - MAPDAMAGE2 found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DAMAGE_RESCALED found in conf/modules.config and Nextflow scripts.
modules_config - PMDTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DAMAGE_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_DAMAGE_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - BAMUTIL_TRIMBAM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DAMAGE_TRIMMED found in conf/modules.config and Nextflow scripts.
modules_config - PRINSEQPLUSPLUS found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
modules_config - CAT_CAT_MALT found in conf/modules.config and Nextflow scripts.
modules_config - UNTAR_METAGENOMICS found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
modules_config - MALTEXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - MEGAN_RMA2INFO found in conf/modules.config and Nextflow scripts.
modules_config - AMPS found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MPILEUP_PILEUPCALLER found in conf/modules.config and Nextflow scripts.
modules_config - SEQUENCETOOLS_PILEUPCALLER found in conf/modules.config and Nextflow scripts.
modules_config - COLLECT_GENOTYPES found in conf/modules.config and Nextflow scripts.
modules_config - EIGENSTRATDATABASETOOLS_EIGENSTRATSNPCOVERAGE found in conf/modules.config and Nextflow scripts.
modules_config - GATK_REALIGNERTARGETCREATOR found in conf/modules.config and Nextflow scripts.
modules_config - GATK_INDELREALIGNER found in conf/modules.config and Nextflow scripts.
modules_config - GATK_UNIFIEDGENOTYPER found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_INDEX_UG found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_HAPLOTYPECALLER found in conf/modules.config and Nextflow scripts.
modules_config - FREEBAYES found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_INDEX_FREEBAYES found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_STATS_GENOTYPING found in conf/modules.config and Nextflow scripts.
modules_config - ANGSD_GL found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.2.1

Run details

nf-core/tools version 3.2.1
Run at 2025-05-09 08:53:49

jfy133 · 2024-04-26T09:17:54Z

jfy133 · 2024-06-28T08:57:14Z

Existing tests to make sure we account for with new configs:

          - "-profile test,docker --preprocessing_tool fastp --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta'"
          - "-profile test,docker --preprocessing_tool adapterremoval --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt' --sequencing_qc_tool falco --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw'"
          - "-profile test,docker --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed'"
          - "-profile test,docker --mapping_tool bowtie2 --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100 --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw'"
          - "-profile test,docker --skip_preprocessing --convert_inputbam"
          - "-profile test_humanbam,docker --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz' --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw'"
          - "-profile test_humanbam,docker --run_sexdeterrmine --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw'"
          - "-profile test_multiref,docker" ## TODO add damage manipulation here instead once it goes multiref

…roblem with collection/name not working

…Dir (but not working - no md5swum?!)

jfy133 · 2024-07-20T07:30:43Z

Ok, just need to sort the lists and then it should work (md5sums are the same but just seem to be out of order)

…ability

nf-core/eager#1063 Co-authored-by: jfy133 <jfy133@users.noreply.github.com> Co-authored-by: nvnieuwk <nvnieuwk@users.noreply.github.com>

…nk so

jfy133 · 2025-03-21T11:20:54Z

Still haven't worked out what is going on, but I've added some debugging prints which should help us where the issue is coming in, the output of nf-test test --tag test --profile test,docker currently looks like :

  �[1mTest�[0m [b63d99d2] 'test_profile' ###################################################################################
UNSTABLE_PATTERNS_AUTH: [**/mapped_reads_gc-content_distribution.txt, **/genome_gc_content_per_window.png, **/*.{svg,pdf,html}, *.{svg,pdf,html}, **/DamageProfiler.log]
DEF: def stable_content_authentication   = getAllFilesFromDir(/home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication    , includeDir: true         , ignore: [**/mapped_reads_gc-content_distribution.txt, **/genome_gc_content_per_window.png, **/*.{svg,pdf,html}, *.{svg,pdf,html}, **/DamageProfiler.log] , ignoreFile: null                 , include: ['*', '**/*'] )
DEF: def stable_name_mapping             = getAllFilesFromDir(/home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/mapping           , includeDir: true         , ignore: null                   , ignoreFile: null                 , include: ['**/*.{bam,bai}'] )
STABLE_CONTENT_AUTHENTICATION: stable_content_authentication: [/home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/bedtools, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/bedtools/stats, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/bedtools/stats/JK2782_Mammoth_MT_Krause_depth.bed, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/bedtools/stats/JK2802_Mammoth_MT_Krause_depth.bed, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/3pGtoA_freq.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/3p_freq_misincorporations.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/5pCtoT_freq.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/5p_freq_misincorporations.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/DNA_comp_genome.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/DNA_composition_sample.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/dmgprof.json, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/editDistance.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/lgdistribution.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause/misincorporation.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause/3pGtoA_freq.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause/3p_freq_misincorporations.txt, /home/james/git/nf-core/eager/.nf-test/tests/b63d99d2cf1c67219d8a9774c87f1ce4/output/authentication/damageprofiler/stats/JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause/5pCtoT_freq.txt, 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###################################################################################

To me it looks like the two lists are being picked up correctly.

My suspicioun is the use of includeDir: true is giving the directory which nf-test will automatically whenever it gets given a directory will piuckup ALL files in it by default, even if you've told the function to exlucde them.

So function works - but we are using it badly by allowing directories to be in the list that is passed to nf-test

jfy133 · 2025-03-21T13:37:00Z

To check: HTML files that @TCLamnidis said was missing

jfy133 · 2025-03-25T06:10:15Z

Possible remaining things:

dedupped bams and flagstat are only in the all_files, not a specific snapshot
filtered_Bams and lengthonly_.filtered.bam are only in the all files, not a specific snapshot

Re added some tests. For some reason, qualimapReport.html keeps failing md5sum checks, even though it should only be picked up in the stable_name test 😖

Also, checksing BAMs with nft-bam is not possible. Headers are unstable due to samtools merge adding @PG tags with randomised names. Headers could be checked for consistency if we tweak the SAMTOOLS_MERGE_LANES process to not retain all @PG tags in the merged BAMs. 🤔

Based on this I'm assuming @TCLamnidis checked that we get variable header AND names, therefore I will just add them to the 'unstable' and check for names system

jfy133 · 2025-03-25T15:38:30Z

I think this is working now! I aded the missing bam/flagstats as just checking for names

TCLamnidis · 2025-04-11T12:22:25Z

Can confirm this snapshot worked. All files are present. I removed some comments and debug outputs. I think this is ready

TCLamnidis · 2025-05-02T16:50:58Z

I updated the nf-test to the new test profile setup.
I also added a (potentially overkill) check for VCF header partial consistency.

The results from authentication still contain some unstable files, but I think that is caused by instability in the underlying BAM files. Not sure how we can fix that, short of filtering the original FastQs and input BAMs to not include any unique reads starting at the same position...

The following files had were unstable in my last local run:

3p_freq_misincorporations.txt
DNA_comp_genome.txt
DNA_composition_sample.txt
misincorporation.txt
genome_results.txt
mapped_reads_nucleotide_content.txt

jfy133

I approve the latest changes, @TCLamnidis I'm the author of this PR so I can't give ✔️ myself

Add general structure, and generate (not working!) snapshot for basic…

f7fceaf

… test profile

jfy133 marked this pull request as draft April 26, 2024 08:57

jfy133 added 2 commits April 26, 2024 13:00

Try adding an ignore zip system, doesn't work atm though...

0778e58

Merge branch 'dev' into nf-test-conversionMerge in from dev

eb73ae6

jfy133 added 10 commits June 28, 2024 13:40

Continue customisation

cc114f3

More debugging

37994df

Get working function

e07dc06

Get working function properly, and start integrating into snapshot: p…

c0f93d9

…roblem with collection/name not working

Extract names properly

de035ca

Remove unnecesary code

7890575

Get working string check function!

b795b9e

TODO

cac8152

Update MQC so works on gitpod, try to re-add original getAllFilesFrom…

a8dcd64

…Dir (but not working - no md5swum?!)

And get it back again

56cba0c

jfy133 added 6 commits July 22, 2024 08:51

Sort output to ensure consistency

0f12b21

Sort file name only funciton

d41aad9

Start testing preprocessing

61c4d24

Merge branch 'dev' into nf-test-conversion

19db88c

Start adding preprocessing dir but diff not working so can't ser vari…

bcc3baf

…ability

Backing up TODO notes

0b58cf7

edmundmiller added a commit to nf-core/nascent that referenced this pull request Aug 10, 2024

test: Add UTILS functions from function guy

4026329

nf-core/eager#1063 Co-authored-by: jfy133 <jfy133@users.noreply.github.com> Co-authored-by: nvnieuwk <nvnieuwk@users.noreply.github.com>

edmundmiller added a commit to nf-core/nascent that referenced this pull request Aug 10, 2024

test: Add UTILS functions from function guy

f5aa9e1

nf-core/eager#1063 Co-authored-by: jfy133 <jfy133@users.noreply.github.com> Co-authored-by: nvnieuwk <nvnieuwk@users.noreply.github.com>

edmundmiller added a commit to nf-core/nascent that referenced this pull request Aug 11, 2024

test: Add UTILS functions from function guy

2d049ff

nf-core/eager#1063 Co-authored-by: jfy133 <jfy133@users.noreply.github.com> Co-authored-by: nvnieuwk <nvnieuwk@users.noreply.github.com>

Final snapshots, need to double check all files are covered but I thi…

eb4824e

…nk so

TCLamnidis added this to the 3.0 Augsburg milestone Sep 6, 2024

Finalise first test

9ce930f

Add ebugging prints

70a1bcf

jfy133 added 2 commits March 21, 2025 12:27

Fix var name

4e4dacb

Update test snapshot to exclude directories and contained files

a71ab62

jfy133 mentioned this pull request Mar 21, 2025

getAllFilesFromDir includeDir and exclude pattern are not comaptible with each other nf-core/nft-utils#33

Open

jfy133 added 2 commits March 25, 2025 07:10

Merge branch 'dev' into nf-test-conversion

07e700b

Add missing bam and flagstat files

2da70df

TCLamnidis mentioned this pull request Apr 11, 2025

DSL2 - Genotyping Input Updates #1126

Open

11 tasks

TCLamnidis added 3 commits April 11, 2025 14:19

remove unused nft-bam plugin

b851b79

cleanup unused code and debug output

fe911fe

Merge branch 'dev' into nf-test-conversion

f647346

TCLamnidis mentioned this pull request May 2, 2025

DSL2: test nf-test conversion #1143

Closed

TCLamnidis added 7 commits May 2, 2025 11:52

Merge branch 'dev' into nf-test-conversion

8b87f81

add bamfiltering_savefilteredbams again

9042f8d

remve duplicate Qualimap config

4735f76

update test. add genotyping and metagenomics

edcad86

update snapshot

744f415

exclude unstable files from md5sum

76d6af4

Stricter checking of VCF file checksums using nft-vcf.

64171ed

add to unstable file list

229b061

jfy133 commented May 9, 2025

View reviewed changes

TCLamnidis added 2 commits May 9, 2025 10:51

better comments

9c78525

add 5p_misincorporation to ignore list

43c6bba

TCLamnidis merged commit 652b0c1 into dev May 9, 2025
18 checks passed

TCLamnidis deleted the nf-test-conversion branch May 9, 2025 09:35

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-eager_logo_dark.png">\n <img alt="nf-core/eager" src="docs/images/nf-core-eager_logo_light.png">\n \n

❔ Tests ignored:

✅ Tests passed:

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Variable output

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jfy133 commented Apr 26, 2024 •

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github-actions bot commented Apr 26, 2024 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️

jfy133 commented Apr 26, 2024 •

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jfy133 commented Mar 21, 2025 •

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