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Add nf-test sharding CI

Add nf-test sharding CI #8

GitHub Actions / JUnit Test Report failed Oct 2, 2024 in 0s

56 tests run, 29 passed, 0 skipped, 27 failed.

Annotations

Check failure on line 1 in Test Process BCFTOOLS_CONCAT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process BCFTOOLS_CONCAT.sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] 

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-74e5df71ed64a22c00e3840c44e13b74.nf` [adoring_fourier] DSL2 - revision: 7fe28f65b0
Downloading plugin [email protected]
Downloading plugin [email protected]
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-74e5df71ed64a22c00e3840c44e13b74.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/74e5df71ed64a22c00e3840c44e13b74/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: 

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-a52a407c15c0da01d05be1c739da58e5.nf` [distracted_yonath] DSL2 - revision: 6443073f16
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-a52a407c15c0da01d05be1c739da58e5.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/a52a407c15c0da01d05be1c739da58e5/meta/nextflow.log' file for more details
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 - 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-44e4658d575ca4d2b322c5468e5b2101.nf` [hopeful_hodgkin] DSL2 - revision: cd4d5087c7
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-44e4658d575ca4d2b322c5468e5b2101.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/44e4658d575ca4d2b322c5468e5b2101/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process BWAMEM2_INDEX

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process BWAMEM2_INDEX.BWAMEM2 index 

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-cee0b72aac42f68c14744e38cad163a4.nf` [awesome_mestorf] DSL2 - revision: 0a4ef2271f
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 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 - 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-4a9ac93358a712ca91dfe1d0ae278d0d.nf` [festering_mirzakhani] DSL2 - revision: 331757ce91
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 - bam 

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-292f1ec56a73660a63c415c9108ee105.nf` [cheesy_wilson] DSL2 - revision: 8d9f70975f
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-292f1ec56a73660a63c415c9108ee105.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/292f1ec56a73660a63c415c9108ee105/meta/nextflow.log' file for more details
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 hybrid mode - bam 

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-3343e7f1553c6a650a18ad130d6c54f7.nf` [shrivelled_gates] DSL2 - revision: d15fa4335c
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-3343e7f1553c6a650a18ad130d6c54f7.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/3343e7f1553c6a650a18ad130d6c54f7/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process DEEPVARIANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process DEEPVARIANT.homo_sapiens - [bam, bai] - 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-20f596fd35698a7d6fcc66585e01b055.nf` [special_morse] DSL2 - revision: b31b3f0947
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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-a127856adaddf53f996e5e276ed73834.nf` [prickly_fermat] 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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-3d5e3a7421bac756b832552a6703e39e.nf` [mad_kay] 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 7 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-c58d2d608195f25faaea707573de3998.nf` [shrivelled_goldstine] DSL2 - revision: 57c09341af
[f4/6a3404] Submitted process > FASTP (test)
Nextflow stderr:

Check failure on line 1 in Test Process FGBIO_FASTQTOBAM

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process FGBIO_FASTQTOBAM.homo_sapiens - [fastq1, fastq2] - bam 

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-896292edc9c5f89c8661330394b08f9f.nf` [nostalgic_lavoisier] DSL2 - revision: c1fb981734
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-896292edc9c5f89c8661330394b08f9f.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/896292edc9c5f89c8661330394b08f9f/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 - [ bam, bai ] - fasta - fai 

Assertion failed: 

4 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-c1f0c01cc4505636ab01fbf576bcb828.nf` [gloomy_shannon] DSL2 - revision: 56f85751a0
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-c1f0c01cc4505636ab01fbf576bcb828.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/c1f0c01cc4505636ab01fbf576bcb828/meta/nextflow.log' file for more details
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 

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-87d2475a2777b4a95aa00a67dc3f7e21.nf` [amazing_hilbert] DSL2 - revision: e17171bd45
[ff/49b180] 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.homo_sapiens - 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-c26593249022e59a5fc168e31f3cd221.nf` [nice_payne] DSL2 - revision: 6513c12b9c
[c3/c34167] Submitted process > GATK4_BASERECALIBRATOR (test)
Nextflow stderr:

Check failure on line 1 in Test Process GATK4_GENOMICSDBIMPORT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4_GENOMICSDBIMPORT.test_gatk4_genomicsdbimport_get_intervalslist 

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-6295e742960e2235da53319c04fc7f8e.nf` [infallible_keller] DSL2 - revision: ade31c482b
[bd/699623] Submitted process > UNTAR (test_genomicsdb.tar.gz)
[d2/95c6a6] Submitted process > GATK4_GENOMICSDBIMPORT (test)
Nextflow stderr:

Check failure on line 1 in Test Process GATK4_MUTECT2

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4_MUTECT2.tumor_normal_pair_f1r2 

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-256de122e4c5afd74af2b60ef7ae8ad1.nf` [hungry_picasso] DSL2 - revision: 9f32c9dc55
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-256de122e4c5afd74af2b60ef7ae8ad1.nf' at line: 39 or see '/home/runner/work/sarek/sarek/.nf-test/tests/256de122e4c5afd74af2b60ef7ae8ad1/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process GATK4_MUTECT2

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process GATK4_MUTECT2.tumor_normal_pair_f1r2_stubs 

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-2485b124332266ea2d75ee1f9b5e9c66.nf` [nasty_lamport] DSL2 - revision: 9f32c9dc55
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-2485b124332266ea2d75ee1f9b5e9c66.nf' at line: 39 or see '/home/runner/work/sarek/sarek/.nf-test/tests/2485b124332266ea2d75ee1f9b5e9c66/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.sarscov2 - bam 

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-c39d9aa5d415aa6f1dd8a64487cbdabf.nf` [romantic_thompson] DSL2 - revision: 1c61d0727e
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-c39d9aa5d415aa6f1dd8a64487cbdabf.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/c39d9aa5d415aa6f1dd8a64487cbdabf/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, [] 

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-5e46c99d36b094824d7f084d29773397.nf` [elegant_faraday] DSL2 - revision: f17f6de824
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-5e46c99d36b094824d7f084d29773397.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/5e46c99d36b094824d7f084d29773397/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, [] - quantized 

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-c01a7d21d5a293f5f254966cbd89a425.nf` [fervent_spence] DSL2 - revision: f17f6de824
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-c01a7d21d5a293f5f254966cbd89a425.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/c01a7d21d5a293f5f254966cbd89a425/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process NGSCHECKMATE_NCM

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process NGSCHECKMATE_NCM.sarscov2 - vcf - 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-ab2fd6a88fa54ec639a8642d5b2cf334.nf` [golden_newton] DSL2 - revision: 58a8f59246
ERROR ~ No such file or directory: Can't find a matching module file for include: /home/runner/work/sarek/sarek/modules/nf-core/ngscheckmate/ncm/tests/../../../bedtools/makewindows/main.nf

 -- Check script '/home/runner/work/sarek/sarek/.nf-test-ab2fd6a88fa54ec639a8642d5b2cf334.nf' at line: 11 or see '/home/runner/work/sarek/sarek/.nf-test/tests/ab2fd6a88fa54ec639a8642d5b2cf334/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Test Process SAMTOOLS_MPILEUP

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SAMTOOLS_MPILEUP.bam_bed 

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-615cee70294843d80f8107b57f14944a.nf` [kickass_lavoisier] DSL2 - revision: 440a351759
Nextflow stderr:

Check failure on line 1 in Test Process SNPEFF_DOWNLOAD

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SNPEFF_DOWNLOAD.test-snpeff-download 

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-f78b29d84b0439fa8c402a1ed50b8735.nf` [suspicious_mccarthy] DSL2 - revision: 629db28a71
Nextflow stderr:

Check failure on line 1 in Test Process STRELKA_GERMLINE

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process STRELKA_GERMLINE.human - cram - 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-d2279dcfa67c382684e12118af4aae2.nf` [gloomy_faggin] DSL2 - revision: c937b3d93a
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram
[6e/d50f1d] Submitted process > STRELKA_GERMLINE (test)
Nextflow stderr:
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