Skip to content
pytest-workflow

Add nf-test sharding CI #18

Sign in to view logs

Add nf-test sharding CI

Add nf-test sharding CI #18

GitHub Actions / JUnit Test Report failed Oct 4, 2024 in 0s

73 tests run, 40 passed, 0 skipped, 33 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, [], annotation, annotation_tbi], [] - vcf_output 

Assertion failed: 

2 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/.nf-test-aa8b62228e7b586f5319cb9f9e3fdcb0.nf` [naughty_legentil] DSL2 - revision: 3bbdce4d42
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-aa8b62228e7b586f5319cb9f9e3fdcb0.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/aa8b62228e7b586f5319cb9f9e3fdcb0/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], [] - stub 

Assertion failed: 

2 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/.nf-test-a8451f450595c5001f45300d6511656.nf` [gloomy_curry] DSL2 - revision: a01a43d4bb
Process `BCFTOOLS_ANNOTATE` declares 4 input channels but 2 were specified

 -- Check script '/home/runner/work/sarek/sarek/.nf-test-a8451f450595c5001f45300d6511656.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/a8451f450595c5001f45300d6511656/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, []], fasta, true 

Assertion failed: 

5 of 6 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-a52a407c15c0da01d05be1c739da58e5.nf` [cheesy_hypatia] DSL2 - revision: 804fd5d270
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 

Assertion failed: 

1 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-db135e932f528e12d7126a44057e4836.nf` [furious_linnaeus] DSL2 - revision: be84272338
[8d/b96464] Submitted process > BCFTOOLS_SORT (test)
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_csi - stub 

Assertion failed: 

1 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-f97631f4fcfca1846f3ea6ba1fd78820.nf` [sleepy_koch] DSL2 - revision: be84272338
[7a/2be2db] Submitted process > BCFTOOLS_SORT (test)
Nextflow stderr:

Check failure on line 1 in Test Process BWA_MEM

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process BWA_MEM.Single-End Sort 

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/.nf-test-42230dbe123df2f99632f6dbe75ece1b.nf` [stoic_legentil] DSL2 - revision: cab0ca230f
[a5/2fd9c2] Submitted process > BWA_INDEX (genome.fasta)
[3b/48d9e9] Submitted process > BWA_MEM (test)
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 - [fastq1, fastq2], index, fasta, true 

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/.nf-test-52fa0d2217318220d5a3490f900f5fa4.nf` [berserk_montalcini] DSL2 - revision: c64d48493d
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 hybrid mode - bam 

java.lang.NullPointerException: Cannot invoke method getAt() on null object
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-fc438db575bababb4a6f66ac343408c6.nf` [jolly_magritte] DSL2 - revision: d080a1761d
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 germline mode - cram 

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/.nf-test-3c695a64203190e2ed69ae6bdc34d119.nf` [jolly_mandelbrot] DSL2 - revision: cd776bec1e
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram
Nextflow stderr:

Check failure on line 1 in Test Process CNVKIT_REFERENCE

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process CNVKIT_REFERENCE.human - [fasta, bed] - stub 

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/.nf-test-ff87ec3fed425dabc30eb6cc831f4c13.nf` [desperate_sammet] DSL2 - revision: 32cd6d5dbc
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
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 - fastq, hashtable, fasta, false 

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/.nf-test-7546220133dde66e0e7726c96703bbdb.nf` [furious_golick] DSL2 - revision: af0c5fcfc5
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_ALIGN

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

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

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/.nf-test-33cb4b8e473cc9b6465709f90895f701.nf` [stoic_knuth] DSL2 - revision: 6e19e71825
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 ENSEMBLVEP_VEP

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process ENSEMBLVEP_VEP.test_ensemblvep_vep_fasta_vcf 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-8a3c673bffc0ddff2c4ab4c88a71ee12.nf` [lethal_ritchie] DSL2 - revision: 3548fcde48
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_trim_fail 

Assertion failed: 

1 of 4 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-9a576f8326ef1386c3e350f64c0c98c5.nf` [tiny_cantor] DSL2 - revision: 062f412c89
[03/b368c9] Submitted process > FASTP (test)
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_qc_only 

Assertion failed: 

2 of 4 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-68e563432bf003338910d8317d706151.nf` [silly_waddington] DSL2 - revision: d71cbba413
[3c/c964d4] Submitted process > FASTP (test)
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 ] - fasta - fai 

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/.nf-test-91365d493da151f62409f8391ca7c59f.nf` [sleepy_mestorf] DSL2 - revision: 05f6b7027f
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 - cram 

Assertion failed: 

1 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-e09b8f6d5dcc6a79c15bbb9fdcc1a2f2.nf` [friendly_heisenberg] DSL2 - revision: 675f8b19b6
[d8/5a5454] Submitted process > GATK4_APPLYBQSR (test)
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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-63bc0bcfcaaaf6949a3cbab722b813a7.nf` [shrivelled_boltzmann] DSL2 - revision: 934fc47b49
[dd/a25ebb] Submitted process > GATK4_BASERECALIBRATOR (test)
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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-22f53e6868c92051c2f62f7b733e3ebb.nf` [curious_wescoff] DSL2 - revision: b5ad5c616e
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam
[a7/ca5109] Submitted process > GATK4_ESTIMATELIBRARYCOMPLEXITY (test)
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_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi 

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/.nf-test-ec14820ffaaed79e89bdd8e06dce953b.nf` [loving_hilbert] DSL2 - revision: 4ba423f236
[26/95f086] Submitted process > UNTAR (test_genomicsdb.tar.gz)
[be/3e6fb2] Submitted process > GATK4_GENOTYPEGVCFS (test)
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 - sites - sites_tbi 

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/.nf-test-1369ef3c6626c54340f532598d7f7596.nf` [cranky_bernard] DSL2 - revision: d30bb998e3
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 intervals 

Assertion failed: 

2 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/.nf-test-19afb6f8c6e46fbb3132ef7bc4dc5f0f.nf` [distracted_golick] DSL2 - revision: b667266299
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-19afb6f8c6e46fbb3132ef7bc4dc5f0f.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/19afb6f8c6e46fbb3132ef7bc4dc5f0f/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 - metrics 

Assertion failed: 

6 of 6 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-fc00cd5fb5ccdd893be5e51d42baa177.nf` [pedantic_wozniak] 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-fc00cd5fb5ccdd893be5e51d42baa177.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/fc00cd5fb5ccdd893be5e51d42baa177/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process LOFREQ_CALLPARALLEL

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process LOFREQ_CALLPARALLEL.sarscov2 - bam 

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/.nf-test-682cc291ef617ee8ef7a24fdfd0b6932.nf` [spontaneous_tesla] DSL2 - revision: cca18b06f0
[26/676157] Submitted process > LOFREQ_CALLPARALLEL (test)
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 - cram, crai, [] 

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/.nf-test-2e48b6a01c7dc2075099bbd7372e81ea.nf` [serene_faraday] DSL2 - revision: b85459c016
[d8/7ea807] Submitted process > MOSDEPTH (test)
Nextflow stderr:
View more details on GitHub Actions