Update ascat module #1922

SPPearce · 2025-06-16T10:45:07Z

Update ASCAT to expose the additional_allelecounter_flags option from the upstream modules repository

github-actions · 2025-06-16T10:47:55Z

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

Posted for pipeline commit 8d6c3cc

+| ✅ 597 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

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 base.config: Check the defaults for all processes
schema_lint - Input mimetype is missing or empty
schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/ci.yml
files_exist - File is ignored: conf/modules.config
nf_test_content - 'tests/samplesheets.nf.test' checking ignored
nf_test_content - 'tests/nextflow.config' checking ignored
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
template_strings - template_strings
modules_config - modules_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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-sarek_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_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: nf-test.config
files_exist - File found: tests/default.nf.test
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: 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
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-sarek_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
files_exist - File not found check: lib/Utils.groovy
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/WorkflowSarek.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: 3.6.0dev
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.step= mapping
nextflow_config - Config default value correct: params.split_fastq= 50000000
nextflow_config - Config default value correct: params.nucleotides_per_second= 200000
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.length_required= 15
nextflow_config - Config default value correct: params.group_by_umi_strategy= Adjacency
nextflow_config - Config default value correct: params.aligner= bwa-mem
nextflow_config - Config default value correct: params.ascat_min_base_qual= 20
nextflow_config - Config default value correct: params.ascat_min_counts= 10
nextflow_config - Config default value correct: params.ascat_min_map_qual= 35
nextflow_config - Config default value correct: params.cf_coeff= 0.05
nextflow_config - Config default value correct: params.cf_contamination= 0
nextflow_config - Config default value correct: params.cf_minqual= 0
nextflow_config - Config default value correct: params.cf_mincov= 0
nextflow_config - Config default value correct: params.cf_ploidy= 2
nextflow_config - Config default value correct: params.sentieon_haplotyper_emit_mode= variant
nextflow_config - Config default value correct: params.sentieon_dnascope_emit_mode= variant
nextflow_config - Config default value correct: params.sentieon_dnascope_pcr_indel_model= CONSERVATIVE
nextflow_config - Config default value correct: params.gatk_pcr_indel_model= CONSERVATIVE
nextflow_config - Config default value correct: params.dbnsfp_fields= rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
nextflow_config - Config default value correct: params.vep_custom_args= --everything --filter_common --per_gene --total_length --offline --format vcf
nextflow_config - Config default value correct: params.vep_version= 111.0-0
nextflow_config - Config default value correct: params.vep_out_format= vcf
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.genome= GATK.GRCh38
nextflow_config - Config default value correct: params.snpeff_cache= s3://annotation-cache/snpeff_cache/
nextflow_config - Config default value correct: params.vep_cache= s3://annotation-cache/vep_cache/
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/sarek3
nextflow_config - Config default value correct: params.seq_platform= ILLUMINA
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/
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_msisensorpro.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alignment_to_fastq.nf.test' contains outdir parameter
nf_test_content - 'tests/alignment_to_fastq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alignment_to_fastq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_ascat.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_ascat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_ascat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_ascat.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_ascat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_ascat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_ascat.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_ascat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_ascat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_ascat.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_ascat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_ascat.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_preparerecalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-dragmap.nf.test' contains outdir parameter
nf_test_content - 'tests/aligner-dragmap.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-dragmap.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-dragmap.nf.test' contains outdir parameter
nf_test_content - 'tests/aligner-dragmap.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-dragmap.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/spark.nf.test' contains outdir parameter
nf_test_content - 'tests/spark.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/spark.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/spark.nf.test' contains outdir parameter
nf_test_content - 'tests/spark.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/spark.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/postprocess_normalization.nf.test' contains outdir parameter
nf_test_content - 'tests/postprocess_normalization.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/postprocess_normalization.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_lofreq.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_lofreq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_lofreq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_lofreq.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_lofreq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_lofreq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/save_mapped.nf.test' contains outdir parameter
nf_test_content - 'tests/save_mapped.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/save_mapped.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_recalibration.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_recalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_recalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_recalibration.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_recalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_recalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_recalibration.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_recalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_recalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_recalibration.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_recalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_recalibration.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon.nf.test' contains outdir parameter
nf_test_content - 'tests/sentieon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/save_output_as_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/save_output_as_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/save_output_as_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mpileup.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_mpileup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mpileup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mpileup.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_mpileup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mpileup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mpileup.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_mpileup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mpileup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mpileup.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_mpileup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mpileup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_merge.nf.test' contains outdir parameter
nf_test_content - 'tests/annotation_merge.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_merge.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_merge.nf.test' contains outdir parameter
nf_test_content - 'tests/annotation_merge.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_merge.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_manta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_bcfann.nf.test' contains outdir parameter
nf_test_content - 'tests/annotation_bcfann.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_bcfann.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_vep.nf.test' contains outdir parameter
nf_test_content - 'tests/annotation_vep.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_vep.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_vep.nf.test' contains outdir parameter
nf_test_content - 'tests/aligner-bwa-mem.nf.test' contains outdir parameter
nf_test_content - 'tests/aligner-bwa-mem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-bwa-mem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-bwa-mem.nf.test' contains outdir parameter
nf_test_content - 'tests/aligner-bwa-mem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-bwa-mem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alignment_from_everything.nf.test' contains outdir parameter
nf_test_content - 'tests/alignment_from_everything.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alignment_from_everything.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/joint_calling_mutect2.nf.test' contains outdir parameter
nf_test_content - 'tests/joint_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/joint_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/joint_calling_mutect2.nf.test' contains outdir parameter
nf_test_content - 'tests/joint_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/joint_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_muse.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_muse.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_muse.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_muse.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_muse.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_muse.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_aligner_bwamem.nf.test' contains outdir parameter
nf_test_content - 'tests/sentieon_aligner_bwamem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_aligner_bwamem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_aligner_bwamem.nf.test' contains outdir parameter
nf_test_content - 'tests/sentieon_aligner_bwamem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_aligner_bwamem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/postprocess_concatenation_normalization.nf.test' contains outdir parameter
nf_test_content - 'tests/postprocess_concatenation_normalization.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/postprocess_concatenation_normalization.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_controlfreec.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-parabricks.nf.test' contains outdir parameter
nf_test_content - 'tests/aligner-parabricks.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-parabricks.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka_bp.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_strelka_bp.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka_bp.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka_bp.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_strelka_bp.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_strelka_bp.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/postprocess_concatenation.nf.test' contains outdir parameter
nf_test_content - 'tests/postprocess_concatenation.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/postprocess_concatenation.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_snpeff.nf.test' contains outdir parameter
nf_test_content - 'tests/annotation_snpeff.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_snpeff.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/annotation_snpeff.nf.test' contains outdir parameter
nf_test_content - 'tests/qc_ngscheckmate.nf.test' contains outdir parameter
nf_test_content - 'tests/qc_ngscheckmate.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/qc_ngscheckmate.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/qc_ngscheckmate.nf.test' contains outdir parameter
nf_test_content - 'tests/qc_ngscheckmate.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/qc_ngscheckmate.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_cnvkit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mutect2.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mutect2.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mutect2.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mutect2.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_mutect2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/joint_calling_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/joint_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/joint_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/joint_calling_haplotypecaller.nf.test' contains outdir parameter
nf_test_content - 'tests/joint_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/joint_calling_haplotypecaller.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-bwa-mem2.nf.test' contains outdir parameter
nf_test_content - 'tests/aligner-bwa-mem2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-bwa-mem2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-bwa-mem2.nf.test' contains outdir parameter
nf_test_content - 'tests/aligner-bwa-mem2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/aligner-bwa-mem2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_markduplicates.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_markduplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_markduplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_markduplicates.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_markduplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_markduplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_markduplicates.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_markduplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_markduplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_markduplicates.nf.test' contains outdir parameter
nf_test_content - 'tests/start_from_markduplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/start_from_markduplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_deepvariant.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/tumor-normal-pair.nf.test' contains outdir parameter
nf_test_content - 'tests/tumor-normal-pair.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/tumor-normal-pair.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_tiddit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_tiddit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_tiddit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_tiddit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_tiddit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_tiddit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_tiddit.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_tiddit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_tiddit.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/preprocessing_umi.nf.test' contains outdir parameter
nf_test_content - 'tests/preprocessing_umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/preprocessing_umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/preprocessing_umi.nf.test' contains outdir parameter
nf_test_content - 'tests/preprocessing_umi.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/fastp.nf.test' contains outdir parameter
nf_test_content - 'tests/fastp.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/fastp.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/fastp.nf.test' contains outdir parameter
nf_test_content - 'tests/fastp.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/fastp.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' contains outdir parameter
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' contains outdir parameter
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' contains outdir parameter
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' contains outdir parameter
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' contains outdir parameter
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' contains outdir parameter
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/intervals.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_dedup.nf.test' contains outdir parameter
nf_test_content - 'tests/sentieon_dedup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_dedup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_dedup.nf.test' contains outdir parameter
nf_test_content - 'tests/sentieon_dedup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_dedup.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_dnascope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
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 - docs/README.md matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: cloudtest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: ncbench.yml
actions_schema_validation - Workflow validation passed: nf-test-gpu.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template-version-comment.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - UNZIP found in conf/base.config and Nextflow scripts.
base_config - FASTQC found in conf/base.config and Nextflow scripts.
base_config - FASTP found in conf/base.config and Nextflow scripts.
base_config - BWAMEM1_MEM found in conf/base.config and Nextflow scripts.
base_config - CNVKIT_BATCH found in conf/base.config and Nextflow scripts.
base_config - GATK4_MARKDUPLICATES found in conf/base.config and Nextflow scripts.
base_config - GATK4_APPLYBQSR found in conf/base.config and Nextflow scripts.
base_config - MOSDEPTH found in conf/base.config and Nextflow scripts.
base_config - STRELKA found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_CONVERT found in conf/base.config and Nextflow scripts.
base_config - GATK4_MERGEVCFS found in conf/base.config and Nextflow scripts.
base_config - MULTIQC found in conf/base.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: 3.3.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.1
Run at 2025-07-03 08:20:42

Changed to v3.2.0

maxulysse · 2025-06-17T13:00:41Z

Can we add some stub tests?

SPPearce · 2025-06-20T14:18:18Z

Added stub tests.
We do have working tests in the modules directory, so in theory we should be able to get something working here.

Update ASCAT module

4137948

SPPearce requested review from FriederikeHanssen and maxulysse as code owners June 16, 2025 10:45

SPPearce changed the base branch from master to dev June 16, 2025 10:45

nf-core deleted a comment from github-actions bot Jun 16, 2025

Update CHANGELOG

bd391ed

maxulysse previously approved these changes Jun 16, 2025

View reviewed changes

Swap to v3.2.0

c592239

SPPearce requested a review from maxulysse June 17, 2025 12:08

SPPearce added 2 commits June 17, 2025 15:39

Add a stub test

9fad8ff

Pull upstream changes and add stub tests

3e0a19e

SPPearce added 2 commits June 20, 2025 14:27

Add modules.json

be8046a

Update ASCAT again from nf-core/modules

c0cdef6

maxulysse added this to the 3.6 milestone Jun 24, 2025

SPPearce added 8 commits June 25, 2025 06:19

Test before updating modules repo yet again

cd541b0

Update directly from modules

a4cc9d3

Merge remote-tracking branch 'origin/dev' into update_ascat_module

b235886

Add non-stub tests

df06e50

Update CHANGELOG

6cb070e

Merge remote-tracking branch 'origin/dev' into update_ascat_module

97f475e

Ignore unstable files

8b1ae13

Explicitly remove the other default ascat files

8d6c3cc

maxulysse approved these changes Jul 3, 2025

View reviewed changes

SPPearce merged commit a8acd1d into dev Jul 3, 2025
40 checks passed

maxulysse deleted the update_ascat_module branch July 14, 2025 13:14

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Update ascat module #1922

Update ascat module #1922

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edited

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maxulysse commented Jun 17, 2025

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Update ascat module #1922

Update ascat module #1922

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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github-actions bot commented Jun 16, 2025 •

edited

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