Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f3de01edee21d550e450c0702aff2f63.nf` [backstabbing_faggin] DSL2 - revision: fa5cb4c1e4
Downloading plugin [email protected]
Downloading plugin [email protected]
WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script '/home/runner/work/sarek/sarek/.nf-test-f3de01edee21d550e450c0702aff2f63.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/f3de01edee21d550e450c0702aff2f63/meta/nextflow.log' file for more details
Nextflow stderr:

Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f052150ac3b66a0383aedd84eb6dbbed.nf` [reverent_jones] DSL2 - revision: 6d5b39f4fc
Core Nextflow options
  runName        : reverent_jones
  containerEngine: docker
  launchDir      : /home/runner/work/sarek/sarek/.nf-test/tests/f052150ac3b66a0383aedd84eb6dbbed
  workDir        : /home/runner/work/sarek/sarek/.nf-test/tests/f052150ac3b66a0383aedd84eb6dbbed/work
  projectDir     : /home/runner/work/sarek/sarek
  userName       : runner
  profile        : test,docker
  configFiles    : 

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

Generic options
  monochrome_logs: true

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
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
* --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/.nf-test/tests/f052150ac3b66a0383aedd84eb6dbbed/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/
* --max_memory: 6.5GB
* --max_cpus: 2
* --max_time: 8.h
* --sentieon_dnascope_model: s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model


WARN: Access to undefined parameter `logo` -- Initialise it to a default value eg. `params.logo = some_value`
WARN: Access to undefined parameter `singularity_pull_docker_container` -- Initialise it to a default value eg. `params.singularity_pull_docker_container = some_value`
Nextflow stderr: