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Add nf-test sharding CI #7

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Add nf-test sharding CI

Add nf-test sharding CI #7

GitHub Actions / JUnit Test Report failed Oct 1, 2024 in 0s

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

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Test pipeline.Run with profile test 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/tests/../main.nf` [amazing_davinci] DSL2 - revision: 1eeed174dc
Downloading plugin [email protected]
Downloading plugin [email protected]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


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

  nf-core/sarek v3.5.0dev
------------------------------------------------------
Core Nextflow options
  runName                   : amazing_davinci
  containerEngine           : docker
  launchDir                 : /home/runner/work/sarek/sarek/.nf-test/tests/a85c00e7ad4e6d012e27cf5869e66973
  workDir                   : /home/runner/work/sarek/sarek/.nf-test/tests/a85c00e7ad4e6d012e27cf5869e66973/work
  projectDir                : /home/runner/work/sarek/sarek
  userName                  : runner
  profile                   : test,docker
  configFiles               : 

Input/output options
  input                     : /home/runner/work/sarek/sarek/tests/csv/3.0/fastq_single.csv
  outdir                    : /home/runner/work/sarek/sarek/.nf-test/tests/a85c00e7ad4e6d012e27cf5869e66973/output

Main options
  split_fastq               : 0
  intervals                 : s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/genome.interval_list
  tools                     : strelka

Annotation
  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

Reference genome options
  genome                    : testdata.nf-core.sarek
  dbsnp                     : s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : s3://ngi-igenomes/testdata/nf-core/modules/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                      : s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/genome.dict
  fasta                     : s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/genome.fasta
  fasta_fai                 : s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/genome.fasta.fai
  germline_resource         : s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz
  germline_resource_tbi     : s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi
  known_indels              : s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz
  known_indels_tbi          : s3://ngi-igenomes/testdata/nf-core/modules/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          : s3://ngi-igenomes/testdata/nf-core/modules/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_genome                : WBcel235
  vep_species               : caenorhabditis_elegans
  vep_cache_version         : 111
  igenomes_base             : s3://ngi-igenomes/testdata/nf-core/modules
  vep_cache                 : null
  snpeff_cache              : null

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function
  modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/

Max job request options
  max_cpus                  : 2
  max_memory                : 6.5GB
  max_time                  : 8.h

Generic options
  validationLenientMode     : true

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/sarek for your analysis please cite:

* 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
------------------------------------------------------
Downloading plugin [email protected]
[8d/4414e4] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L1)
[fe/fb1c43] Submitted process > NFCORE_SAREK:SAREK:FASTQC (test-test_L2)
[41/7b4b47] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED (genome.interval_list)
[d8/b28ed6] Submitted process > NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX (genome.fasta)
[cc/d99c86] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome)
[34/58634d] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test-test_L1)
[fb/0f9f6c] Submitted process > NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (test-test_L2)
[7e/4dd870] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT (chr22_1-40001)
[a3/aa0453] Submitted process > NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (genome)
[56/1fd1a4] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (test)
[38/5b5e4e] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (test)
[c0/614fb9] Submitted process > NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (test)
[36/c6cac2] Submitted process > NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (test)
[86/6b7084] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (test)
[1f/b260e1] Submitted process > NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM (test)
[36/631c7c] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS (test)
[8b/e074dd] Submitted process > NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH (test)
[63/6912fe] Submitted process > NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SINGLE_STRELKA:STRELKA_SINGLE (test)
[f7/94ecad] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS (test)
[2d/013c94] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_QUAL (test)
[e4/04486a] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_SUMMARY (test)
[52/14fb6c] Submitted process > NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:VCFTOOLS_TSTV_COUNT (test)
[08/e43f26] Submitted process > NFCORE_SAREK:SAREK:MULTIQC
-[nf-core/sarek] Pipeline completed successfully-
Nextflow stderr:
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