Nextflow stdout:

N E X T F L O W  ~  version 24.10.0
Launching `/home/runner/work/sarek/sarek/.nf-test-fd9b6cdc0b73bdf8931311b80f631423.nf` [loving_swartz] DSL2 - revision: a141d7fc24
Downloading plugin [email protected]

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  nf-core/sarek 3.5.0dev
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Input/output options
  outdir         : 1
  test_data_base : https://raw.githubusercontent.com/nf-core/test-datasets/sarek3

Core Nextflow options
  runName        : loving_swartz
  containerEngine: docker
  launchDir      : /home/runner/work/sarek/sarek/~/tests/fd9b6cdc0b73bdf8931311b80f631423
  workDir        : /home/runner/work/sarek/sarek/~/tests/fd9b6cdc0b73bdf8931311b80f631423/work
  projectDir     : /home/runner/work/sarek/sarek
  userName       : runner
  profile        : test,docker
  configFiles    : 

!! Only displaying parameters that differ from the pipeline defaults !!
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* The pipeline
    https://doi.org/10.12688/f1000research.16665.2
    https://doi.org/10.1093/nargab/lqae031
    https://doi.org/10.5281/zenodo.3476425

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/sarek/blob/master/CITATIONS.md

WARN: The following invalid input values have been detected:

* --input: /home/runner/work/sarek/sarek/tests/csv/3.0/fastq_single.csv
* --input_restart: null
* --step: mapping
* --genome: testdata.nf-core.sarek
* --igenomes_base: s3://ngi-igenomes/testdata/nf-core/modules
* --snpeff_cache: null
* --vep_cache: null
* --igenomes_ignore: false
* --save_reference: false
* --build_only_index: false
* --download_cache: false
* --no_intervals: false
* --nucleotides_per_second: 200000
* --tools: strelka
* --skip_tools: null
* --split_fastq: 0
* --trim_fastq: false
* --clip_r1: 0
* --clip_r2: 0
* --three_prime_clip_r1: 0
* --three_prime_clip_r2: 0
* --trim_nextseq: 0
* --length_required: 15
* --save_trimmed: false
* --save_split_fastqs: false
* --umi_read_structure: null
* --group_by_umi_strategy: Adjacency
* --aligner: bwa-mem
* --use_gatk_spark: null
* --save_mapped: false
* --save_output_as_bam: false
* --seq_center: null
* --seq_platform: ILLUMINA
* --ascat_ploidy: null
* --ascat_min_base_qual: 20
* --ascat_min_counts: 10
* --ascat_min_map_qual: 35
* --ascat_purity: null
* --cf_ploidy: 2
* --cf_coeff: 0.05
* --cf_contamination: 0
* --cf_contamination_adjustment: false
* --cf_mincov: 0
* --cf_minqual: 0
* --cf_window: null
* --cnvkit_reference: null
* --concatenate_vcfs: false
* --ignore_soft_clipped_bases: false
* --joint_germline: false
* --joint_mutect2: false
* --only_paired_variant_calling: false
* --sentieon_dnascope_emit_mode: variant
* --sentieon_dnascope_pcr_indel_model: CONSERVATIVE
* --sentieon_haplotyper_emit_mode: variant
* --wes: false
* --bcftools_annotations: s3://ngi-igenomes/testdata/nf-core/modules//genomics/sarscov2/illumina/vcf/test2.vcf.gz
* --bcftools_annotations_tbi: s3://ngi-igenomes/testdata/nf-core/modules//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
* --bcftools_header_lines: /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt
* --dbnsfp: null
* --dbnsfp_consequence: null
* --dbnsfp_fields: rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
* --dbnsfp_tbi: null
* --outdir_cache: null
* --spliceai_indel: null
* --spliceai_indel_tbi: null
* --spliceai_snv: null
* --spliceai_snv_tbi: null
* --vep_custom_args: --everything --filter_common --per_gene --total_length --offline --format vcf
* --vep_dbnsfp: null
* --vep_include_fasta: false
* --vep_loftee: null
* --vep_out_format: vcf
* --vep_spliceai: null
* --vep_spliceregion: null
* --vep_version: 111.0-0
* --multiqc_config: null
* --multiqc_title: null
* --multiqc_logo: null
* --max_multiqc_email_size: 25.MB
* --multiqc_methods_description: null
* --email: null
* --email_on_fail: null
* --plaintext_email: false
* --hook_url: null
* --help_full: false
* --show_hidden: false
* --pipelines_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/
* --config_profile_name: Test profile
* --config_profile_description: Minimal test dataset to check pipeline function
* --custom_config_version: master
* --nf_test_output: /home/runner/work/sarek/sarek/~/tests/fd9b6cdc0b73bdf8931311b80f631423/meta
* --custom_config_base: https://raw.githubusercontent.com/nf-core/configs/master
* --config_profile_contact: null
* --config_profile_url: null
* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/
* --sentieon_dnascope_model: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model


Nextflow stderr: