Add Sentieon TNscope #1934

SPPearce · 2025-07-03T14:19:21Z

Adding the Sentieon tumour/normal caller TNscope as a new tool. Can be used in tumour only or tumour/normal modes.

PR checklist

github-actions · 2025-07-03T14:22:34Z

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

Posted for pipeline commit 6f50d5a

+| ✅ 609 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!

Details

❗ 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/variant_calling_sentieon_tnscope.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' contains outdir parameter
nf_test_content - 'tests/variant_calling_sentieon_tnscope.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/variant_calling_sentieon_tnscope.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
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nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
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nf_test_content - 'tests/variant_calling_freebayes.nf.test' snapshots a 'versions.yml' file
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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
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nf_test_content - 'tests/annotation_vep.nf.test' snapshots a 'versions.yml' file
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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
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nf_test_content - 'tests/alignment_from_everything.nf.test' snapshots a 'versions.yml' file
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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 19:28:18

CHANGELOG.md

Co-authored-by: Maxime U Garcia <[email protected]>

maxulysse

Looking good, I'll update the METRO MAP

maxulysse · 2025-07-03T16:05:33Z

you seem to have a discrepancy in the tests

SPPearce · 2025-07-03T19:26:31Z

you seem to have a discrepancy in the tests

Yeah, I added the 2 tumour one but forgot to rename it and hence overwrote the snapshot, and then tried to undo that and manually fix it. Clearly didn't manage properly.

SPPearce added 10 commits April 11, 2025 11:42

First attempt

8861413

Update schema

e45e04a

add module

84b479b

Swap sentieon container

474b111

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

34a45d1

Update tnscope

42e10f7

Merge branch 'tnscope' of https://github.com/nf-core/sarek into tnscope

6ca0e50

Add test skeleton

9b5bc36

Add tumour only, tests and docs

c85777d

Merge branch 'tnscope' of github.com:SPPearce/sarek into tnscope

c320f29

SPPearce requested review from FriederikeHanssen and maxulysse as code owners July 3, 2025 14:19

SPPearce added 2 commits July 3, 2025 15:32

Anonymous AWS access again

198ddb8

Prettier

3953397

maxulysse reviewed Jul 3, 2025

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

SPPearce and others added 2 commits July 3, 2025 15:48

Define empty vcf_tnscope channel

ba60782

Update CHANGELOG.md

f7d1cd5

Co-authored-by: Maxime U Garcia <[email protected]>

maxulysse reviewed Jul 3, 2025

View reviewed changes

Update snapshot

6f50d5a

maxulysse approved these changes Jul 4, 2025

View reviewed changes

maxulysse merged commit 2daa8b4 into dev Jul 4, 2025
70 of 72 checks passed

maxulysse deleted the tnscope branch July 4, 2025 06:47

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Add Sentieon TNscope #1934

Add Sentieon TNscope #1934

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SPPearce commented Jul 3, 2025

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github-actions bot commented Jul 3, 2025 •

edited

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❗ Test warnings:

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Add Sentieon TNscope #1934

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SPPearce commented Jul 3, 2025

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Jul 3, 2025

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SPPearce commented Jul 3, 2025

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github-actions bot commented Jul 3, 2025 •

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