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Add nf-test sharding CI #27

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Add nf-test sharding CI

Add nf-test sharding CI #27

GitHub Actions / JUnit Test Report failed Oct 8, 2024 in 0s

73 tests run, 39 passed, 0 skipped, 34 failed.

Annotations

Check failure on line 1 in Test Process BCFTOOLS_ANNOTATE

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi 

Assertion failed: 

3 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-b585981dd3b0690fed7881e81b047773.nf` [furious_heyrovsky] DSL2 - revision: a01a43d4bb
Downloading plugin [email protected]
Downloading plugin [email protected]
Downloading plugin [email protected]
Process `BCFTOOLS_ANNOTATE` declares 4 input channels but 2 were specified

 -- Check script '/home/runner/work/sarek/sarek/.nf-test-b585981dd3b0690fed7881e81b047773.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/b585981dd3b0690fed7881e81b047773/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process BCFTOOLS_ANNOTATE

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub 

Assertion failed: 

3 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f2f1b70c46365389c1af72aaa239d04b.nf` [deadly_kalman] DSL2 - revision: a01a43d4bb
Process `BCFTOOLS_ANNOTATE` declares 4 input channels but 2 were specified

 -- Check script '/home/runner/work/sarek/sarek/.nf-test-f2f1b70c46365389c1af72aaa239d04b.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/f2f1b70c46365389c1af72aaa239d04b/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process BCFTOOLS_MPILEUP

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, bed], fasta, false 

Assertion failed: 

4 of 5 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f3a09604dc6e16eeca9e34b021a2130f.nf` [modest_hamilton] DSL2 - revision: 9f99721e09
Nextflow stderr:

Check failure on line 1 in Test Process BCFTOOLS_SORT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_tbi 

Assertion failed: 

1 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-a92ae67312258e3ab00345cbfad5f80e.nf` [furious_kalman] DSL2 - revision: be84272338
[64/8a0972] Submitted process > BCFTOOLS_SORT (test)
WARN: Process `BCFTOOLS_SORT` publishDir path contains a variable with a null value
Nextflow stderr:

Check failure on line 1 in Test Process BWAMEM2_MEM

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process BWAMEM2_MEM.sarscov2 - fastq, index, fasta, false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-ed4be5f8101e3149a8f921495eb18bd1.nf` [awesome_feynman] DSL2 - revision: 6cf6ebac0b
WARN: Access to undefined parameter `bwamem2` -- Initialise it to a default value eg. `params.bwamem2 = some_value`
Nextflow stderr:

Check failure on line 1 in Test Process CNVKIT_BATCH

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process CNVKIT_BATCH.cnvkit batch wgs - cram 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-8b9fbda3a86982967a817867f87058c9.nf` [pensive_dubinsky] DSL2 - revision: 95dfc7498d
Nextflow stderr:

Check failure on line 1 in Test Process CNVKIT_BATCH

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process CNVKIT_BATCH.cnvkit batch pon mode - bam 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-996f7ae2066691a85efc1f62237ee0a0.nf` [trusting_brattain] DSL2 - revision: 4da7ce5f61
Nextflow stderr:

Check failure on line 1 in Test Process CNVKIT_GENEMETRICS

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process CNVKIT_GENEMETRICS.test-cnvkit-genemetrics-with-cns 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-d86a1b858dbff119247dc6f16735d51f.nf` [insane_ritchie] DSL2 - revision: d7e0e6314a
Nextflow stderr:

Check failure on line 1 in Test Process CONTROLFREEC_ASSESSSIGNIFICANCE

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process CONTROLFREEC_ASSESSSIGNIFICANCE.human - freec_ratio - stub 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f3a6934daa452cc8cd0beaeaa64eafda.nf` [scruffy_austin] DSL2 - revision: 66b9d3a038
[0b/0cfe91] Submitted process > UNTAR (chromosomes.tar.gz)
WARN: Process `UNTAR` publishDir path contains a variable with a null value
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz
[64/1131dd] Submitted process > CONTROLFREEC_FREEC (test)
WARN: Process `CONTROLFREEC_FREEC` publishDir path contains a variable with a null value
[d3/3a8d7b] Submitted process > CONTROLFREEC_ASSESSSIGNIFICANCE (test)
WARN: Process `CONTROLFREEC_ASSESSSIGNIFICANCE` publishDir path contains a variable with a null value
Nextflow stderr:

Check failure on line 1 in Test Process DEEPVARIANT_RUNDEEPVARIANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [cram, crai, genome_bed] - fasta - fai 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-55517b61b9cb0cae806dc65e7afc316a.nf` [grave_church] DSL2 - revision: 518d773ebb
Nextflow stderr:

Check failure on line 1 in Test Process DRAGMAP_ALIGN

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process DRAGMAP_ALIGN.sarscov2 - [fastq1, fastq2], hashtable, fasta, false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-a127856adaddf53f996e5e276ed73834.nf` [hungry_yalow] DSL2 - revision: 6dceb8565a
WARN: Access to undefined parameter `dragmap` -- Initialise it to a default value eg. `params.dragmap = some_value`
Nextflow stderr:

Check failure on line 1 in Test Process DRAGMAP_HASHTABLE

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process DRAGMAP_HASHTABLE.sarscov2 - fasta - stub 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-3d5e3a7421bac756b832552a6703e39e.nf` [golden_swanson] DSL2 - revision: 65bc0aca92
WARN: Access to undefined parameter `dragmap` -- Initialise it to a default value eg. `params.dragmap = some_value`
Nextflow stderr:

Check failure on line 1 in Test Process FASTP

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process FASTP.test_fastp_single_end 

Assertion failed: 

1 of 4 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-c58d2d608195f25faaea707573de3998.nf` [kickass_khorana] DSL2 - revision: 9c239b6cfe
[c0/11b90e] Submitted process > FASTP (test)
WARN: Process `FASTP` publishDir path contains a variable with a null value
WARN: Process `FASTP` publishDir path contains a variable with a null value
Nextflow stderr:

Check failure on line 1 in Test Process FASTP

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process FASTP.test_fastp_paired_end_merged 

Assertion failed: 

2 of 4 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-e4d55a527e99e7049f3a388d80d0a282.nf` [high_meninsky] DSL2 - revision: e957de6de3
[06/cd5e86] Submitted process > FASTP (test)
WARN: Process `FASTP` publishDir path contains a variable with a null value
WARN: Process `FASTP` publishDir path contains a variable with a null value
Nextflow stderr:

Check failure on line 1 in Test Process FGBIO_CALLMOLECULARCONSENSUSREADS

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process FGBIO_CALLMOLECULARCONSENSUSREADS.homo_sapiens - bam 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-560c5f92a229a858d3ed8ba8b386726d.nf` [confident_jepsen] DSL2 - revision: 797542d3d3
ERROR ~ No such file or directory: Can't find a matching module file for include: /home/runner/work/sarek/sarek/modules/nf-core/fgbio/callmolecularconsensusreads/tests/../../sortbam/main.nf

 -- Check script '/home/runner/work/sarek/sarek/.nf-test-560c5f92a229a858d3ed8ba8b386726d.nf' at line: 11 or see '/home/runner/work/sarek/sarek/.nf-test/tests/560c5f92a229a858d3ed8ba8b386726d/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process FREEBAYES

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process FREEBAYES.sarscov2 - [ cram, crai, cram, crai, bed ] - fasta - fai 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-b63773b2e77ac99761d31388d20d5850.nf` [confident_edison] DSL2 - revision: a0eec4e010
Nextflow stderr:

Check failure on line 1 in Test Process GATK4_APPLYBQSR

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4_APPLYBQSR.sarscov2 - bam - stub 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-c36f0a9b54b0a1b04d2bbe19062dd92b.nf` [happy_lamarr] DSL2 - revision: e17171bd45
[b2/a69a53] Submitted process > GATK4_APPLYBQSR (test)
WARN: Process `GATK4_APPLYBQSR` publishDir path contains a variable with a null value
Nextflow stderr:

Check failure on line 1 in Test Process GATK4_BASERECALIBRATOR

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam - intervals 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-63bc0bcfcaaaf6949a3cbab722b813a7.nf` [disturbed_northcutt] DSL2 - revision: 934fc47b49
[87/2b2f3a] Submitted process > GATK4_BASERECALIBRATOR (test)
WARN: Process `GATK4_BASERECALIBRATOR` publishDir path contains a variable with a null value
Nextflow stderr:

Check failure on line 1 in Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.homo_sapiens - bam 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-22f53e6868c92051c2f62f7b733e3ebb.nf` [modest_shannon] DSL2 - revision: b5ad5c616e
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam
[63/ba265f] Submitted process > GATK4_ESTIMATELIBRARYCOMPLEXITY (test)
WARN: Process `GATK4_ESTIMATELIBRARYCOMPLEXITY` publishDir path contains a variable with a null value
Nextflow stderr:

Check failure on line 1 in Test Process GATK4_GENOTYPEGVCFS

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-3f64474cba964cc95994d9e9115e4b02.nf` [infallible_magritte] DSL2 - revision: 4bcf5cb633
[83/db76a9] Submitted process > UNTAR (test_genomicsdb.tar.gz)
[0c/98f462] Submitted process > GATK4_GENOTYPEGVCFS (test)
WARN: Process `UNTAR` publishDir path contains a variable with a null value
Nextflow stderr:

Check failure on line 1 in Test Process GATK4_HAPLOTYPECALLER

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai] - fasta - fai - dict 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-ee524f4f94e71e0e20e07d452c97cc36.nf` [shrivelled_rutherford] DSL2 - revision: d346f28285
Nextflow stderr:

Check failure on line 1 in Test Process GATK4SPARK_APPLYBQSR

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-c89e246cda82587cacddd788d34b43fb.nf` [nasty_varahamihira] DSL2 - revision: 753a2d256e
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-c89e246cda82587cacddd788d34b43fb.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/c89e246cda82587cacddd788d34b43fb/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process GATK4SPARK_MARKDUPLICATES

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - bam - multiple 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-734baa670beda97ecfabe2c8128e29ea.nf` [festering_stone] DSL2 - revision: 2d9890cd5f
WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'homo_sapiens' on null object

 -- Check script '/home/runner/work/sarek/sarek/.nf-test-734baa670beda97ecfabe2c8128e29ea.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/734baa670beda97ecfabe2c8128e29ea/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process MOSDEPTH

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process MOSDEPTH.homo_sapiens - bam, bai, bed 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-c2423a8b537d45b97e5a929140ee419e.nf` [crazy_rubens] DSL2 - revision: 21553285ad
ERROR ~ Error executing process > 'MOSDEPTH'

Caused by:
  '--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition -- Check script '/home/runner/work/sarek/sarek/modules/nf-core/mosdepth/tests/../main.nf' at line: 38


Source block:
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def reference = fasta ? "--fasta ${fasta}" : ""
  def interval = bed ? "--by ${bed}" : ""
  if (bed && args.contains("--by")) {
      error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
  }
  if (!bed && args.contains("--thresholds")) {
      error "'--thresholds' can only be specified in conjunction with '--by'"
  }
  """
  mosdepth \\
      --threads $task.cpus \\
      $interval \\
      $reference \\
      $args \\
      $prefix \\
      $bam
  
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
      mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
  END_VERSIONS
  """

Container:
  quay.io/biocontainers/mosdepth:0.3.8--hd299d5a_0

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '/home/runner/work/sarek/sarek/.nf-test/tests/c2423a8b537d45b97e5a929140ee419e/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process MOSDEPTH

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process MOSDEPTH.homo_sapiens - bam, bai, bed - thresholds 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-9d435a0ca7acbc55e4bd514b5656ffbb.nf` [admiring_kirch] DSL2 - revision: 21553285ad
ERROR ~ Error executing process > 'MOSDEPTH'

Caused by:
  '--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition -- Check script '/home/runner/work/sarek/sarek/modules/nf-core/mosdepth/tests/../main.nf' at line: 38


Source block:
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def reference = fasta ? "--fasta ${fasta}" : ""
  def interval = bed ? "--by ${bed}" : ""
  if (bed && args.contains("--by")) {
      error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
  }
  if (!bed && args.contains("--thresholds")) {
      error "'--thresholds' can only be specified in conjunction with '--by'"
  }
  """
  mosdepth \\
      --threads $task.cpus \\
      $interval \\
      $reference \\
      $args \\
      $prefix \\
      $bam
  
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
      mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
  END_VERSIONS
  """

Container:
  quay.io/biocontainers/mosdepth:0.3.8--hd299d5a_0

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/.nf-test/tests/9d435a0ca7acbc55e4bd514b5656ffbb/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:
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