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Release 3.5.1 #1799

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merged 13 commits into from
Feb 18, 2025

Update .github/workflows/cloudtest.yml

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Merged

Release 3.5.1 #1799

Update .github/workflows/cloudtest.yml
04cbd12
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GitHub Actions / JUnit Test Report failed Feb 17, 2025 in 0s

8 tests run, 6 passed, 0 skipped, 2 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 merge 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 25.01.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [cranky_cajal] DSL2 - revision: 3954909713

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

  nf-core/sarek 3.5.1
------------------------------------------------------
Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/vcf_single.csv
  step                      : annotate
  outdir                    : /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/output

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

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
  dbsnp                     : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/vcf/dbsnp_146.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/genome.fasta
  fasta_fai                 : https://raw.githubusercontent.com/nf-core/test-datasets/modules/data//genomics/homo_sapiens/genome/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_db                 : WBcel235.105
  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                   : cranky_cajal
  launchDir                 : /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982
  workDir                   : /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,conda
  configFiles               : /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/conf/test.config

!! 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

Staging foreign file: s3://annotation-cache/snpeff_cache/WBcel235.105
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../../nf-core/vcf_annotate_snpeff/../../../modules/nf-core/snpeff/snpeff/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-f166f6710d1284fe-45d87f58d9b67245610a395695fff284]
[f5/92bab9] Submitted process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (test)
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../../nf-core/vcf_annotate_snpeff/../../../modules/nf-core/tabix/bgziptabix/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-5a9ba0ebb7bcf86c-497b0f18c811c5671b5e17e0034188ed]
[48/3da19d] Submitted process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX (test)
Staging foreign file: s3://annotation-cache/vep_cache/113_WBcel235
Creating env using conda: /home/runner/work/sarek/sarek/./workflows/sarek/../../subworkflows/local/vcf_annotate_all/../../nf-core/vcf_annotate_ensemblvep/../../../modules/nf-core/ensemblvep/vep/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134]
[66/b6be39] Submitted process > NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP (test)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP (test)'

Caused by:
  Process `NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP (test)` terminated with an error exit status (2)


Command executed:

  vep \
      -i test_snpEff.ann.vcf.gz \
      -o test_snpEff_VEP.ann.vcf.gz \
      --stats_file test_snpEff_VEP.ann.summary.html      --vcf --everything --filter_common --per_gene --total_length --offline --format vcf \
      --compress_output bgzip \
       \
      --assembly WBcel235 \
      --species caenorhabditis_elegans \
      --cache \
      --cache_version 113 \
      --dir_cache ${PWD}/113_WBcel235 \
      --fork 4
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP":
      ensemblvep: $( echo $(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*$//')
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
  Can't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0 /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/5.32/site_perl /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/site_perl /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/5.32/vendor_perl /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/5.32/core_perl /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/core_perl .) at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 102.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 102.
  Compilation failed in require at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
  Compilation failed in require at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl/base.pm line 100.
  	...propagated at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl/base.pm line 109.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 56.
  Compilation failed in require at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl/base.pm line 100.
  	...propagated at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/lib/perl5/vendor_perl/base.pm line 109.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/share/ensembl-vep-113.0-0/modules/Bio/EnsEMBL/VEP/Runner.pm line 71.
  Compilation failed in require at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/bin/vep line 20.
  BEGIN failed--compilation aborted at /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/conda/env-6938a7a53ac74f6f-d193c4ca26f3953833a160c8d2762134/bin/vep line 20.

Work dir:
  /home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/work/66/b6be39ac4c3c19f6e762bd1d1e7188

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '/home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/sarek/sarek/~/tests/46991b45cbda2e191e8723e7f9b67982/meta/nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-
Nextflow stderr:

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 25.01.0-edge
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [special_legentil] DSL2 - revision: 3954909713

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

  nf-core/sarek 3.5.1
------------------------------------------------------
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                   : special_legentil
  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               : /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/nextflow.config, /home/runner/work/sarek/sarek/conf/test.config

!! 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/samtools/stats/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-1abf3db016bf3fb9-873a3583ebab040412cb72c07ed757ab]
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/mosdepth/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-c5b497d07713b814-57cd7e91fe23a8ceb488416c37dae89b]
[5b/be0bae] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (no_intervals)
[99/386d29] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (sample2)
[5f/cce105] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP (sample2)
[de/27515f] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (sample2)
[17/1e51c8] Submitted process > NFCORE_SAREK:PREPARE_GENOME:UNTAR_CHR_DIR (chromosomes.tar.gz)
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]
[99/568291] 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/freec2circos/environment.yml [cache /home/runner/work/sarek/sarek/~/tests/7d37fa14f56e078ada43e06e51c2d1c1/work/conda/env-4e8926983677b285-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]
[36/ff5640] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:MAKEGRAPH2 (sample2)
[b2/70105a] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:ASSESS_SIGNIFICANCE (sample2)
[45/9c6ca4] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC:FREEC2CIRCOS (sample2)
[97/557706] 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]
[05/508a72] Submitted process > NFCORE_SAREK:SAREK:MULTIQC
-[nf-core/sarek] Pipeline completed successfully-
Nextflow stderr:
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