Skip to content
nf-core CI

Merge pull request #1754 from FriederikeHanssen/fixtest #6626

Sign in to view logs

Merge pull request #1754 from FriederikeHanssen/fixtest

Merge pull request #1754 from FriederikeHanssen/fixtest #6626

GitHub Actions / JUnit Test Report failed Dec 11, 2024 in 0s

8 tests run, 7 passed, 0 skipped, 1 failed.

Annotations

Check failure on line 1 in Test pipeline

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline.Run with profile test | --tools controlfreec --no_intervals | tumoronly 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.11.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [zen_cantor] DSL2 - revision: 3954909713

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek 3.5.0
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/recalibrated_tumoronly.csv
  step                      : variant_calling
  outdir                    : /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/output

Main options
  split_fastq               : 0
  intervals                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.interval_list
  no_intervals              : true
  wes                       : true
  tools                     : controlfreec

Annotation
  bcftools_annotations      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz
  bcftools_annotations_tbi  : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi
  bcftools_header_lines     : /home/runner/work/sarek/sarek/tests/config/bcfann_test_header.txt

General reference genome options
  igenomes_base             : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Reference genome options
  genome                    : testdata.nf-core.sarek
  chr_dir                   : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/genome.dict
  fasta                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai
  germline_resource         : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi
  known_indels_vqsr         : --resource:mills,known=false,training=true,truth=true,prior=10.0 mills_and_1000G.indels.vcf.gz
  ngscheckmate_bed          : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed
  sentieon_dnascope_model   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
  snpeff_cache              : null
  snpeff_db                 : WBcel235.105
  vep_cache                 : null
  vep_cache_version         : 113
  vep_genome                : WBcel235
  vep_species               : caenorhabditis_elegans

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/

Core Nextflow options
  runName                   : zen_cantor
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1
  workDir                   : /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* 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

Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_intervals/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
Creating env using conda: /home/runner/work/sarek/sarek/./subworkflows/local/prepare_genome/../../../modules/nf-core/untar/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-e454bec5a9fe6279-cac18ad63488da9f5109ab1f794a29f6]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_tumor_only_all/../bam_variant_calling_mpileup/../../../modules/nf-core/samtools/mpileup/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-298b77ab5b2fec3c-873a3583ebab040412cb72c07ed757ab]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/cram_sampleqc/../../../subworkflows/local/cram_qc_mosdepth_samtools/../../../modules/nf-core/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
[0b/a8c536] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (no_intervals)
[b1/6f836d] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample2)
[a0/ae7a39] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP (sample2)
[a1/db2868] Submitted process > NFCORE_SAREK:PREPARE_GENOME:UNTAR_CHR_DIR (chromosomes.tar.gz)
[2a/0a35c0] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample2)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_tumor_only_all/../bam_variant_calling_tumor_only_controlfreec/../../../modules/nf-core/controlfreec/freec/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-538bcdb3bc8da9e4-b045b606f9dcfe6897fe2c50e0f58bc7]
[65/25f178] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC_TUMORONLY (sample2)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_tumor_only_all/../bam_variant_calling_tumor_only_controlfreec/../../../modules/nf-core/controlfreec/makegraph2/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-5c584a792008796d-b045b606f9dcfe6897fe2c50e0f58bc7]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_tumor_only_all/../bam_variant_calling_tumor_only_controlfreec/../../../modules/nf-core/controlfreec/freec2bed/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-00cc74a07c8305aa-b045b606f9dcfe6897fe2c50e0f58bc7]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_tumor_only_all/../bam_variant_calling_tumor_only_controlfreec/../../../modules/nf-core/controlfreec/assesssignificance/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-ab3c40235a741d77-5b84389ee299f53755a38d176aa5b217]
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_tumor_only_all/../bam_variant_calling_tumor_only_controlfreec/../../../modules/nf-core/controlfreec/freec2circos/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-4e8926983677b285-b045b606f9dcfe6897fe2c50e0f58bc7]
[df/af4cb9] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:MAKEGRAPH2 (sample2)
[c1/f40945] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC2CIRCOS (sample2)
[28/9f2414] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:ASSESS_SIGNIFICANCE (sample2)
[76/7de68a] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC2BED (sample2)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../modules/nf-core/multiqc/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-7da4088df3b01749-eec4e05336245ea50db6412788f8c4da]
[b9/86d525] Submitted process > NFCORE_SAREK:SAREK:MULTIQC
-[nf-core/sarek] Pipeline completed successfully-
Nextflow stderr:
View more details on GitHub Actions