Add nf-test sharding CI #7
56 tests run, 27 passed, 0 skipped, 29 failed.
Annotations
Check failure on line 1 in Test Process BCFTOOLS_ANNOTATE
github-actions / JUnit Test Report
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, [], [], [], header] - bcf_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-91799993e6cb159e777f6d4c73138816.nf` [fervent_varahamihira] DSL2 - revision: a9b8486a22
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 'sarscov2' on null object
-- Check script '/home/runner/work/sarek/sarek/.nf-test-91799993e6cb159e777f6d4c73138816.nf' at line: 33 or see '/home/runner/work/sarek/sarek/.nf-test/tests/91799993e6cb159e777f6d4c73138816/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process BCFTOOLS_MPILEUP
github-actions / JUnit Test Report
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, []], fasta, false
Assertion failed:
5 of 5 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-8ac76e42363269bbc2f145695ad2fae4.nf` [angry_murdock] DSL2 - revision: 9ad4c17419
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-8ac76e42363269bbc2f145695ad2fae4.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/8ac76e42363269bbc2f145695ad2fae4/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process BCFTOOLS_MPILEUP
github-actions / JUnit Test Report
Test Process BCFTOOLS_MPILEUP.sarscov2 - [bam, bed], fasta, false stub
Assertion failed:
5 of 5 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-1a5f0352cead0d009265ad64db0f029e.nf` [infallible_shockley] DSL2 - revision: 7162872f6f
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-1a5f0352cead0d009265ad64db0f029e.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/1a5f0352cead0d009265ad64db0f029e/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process BWAMEM2_MEM
github-actions / JUnit Test Report
Test Process BWAMEM2_MEM.sarscov2 - [fastq1, fastq2], index, 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-7136dedfcfcc8e5e0e35f11b11b79c8.nf` [jovial_church] DSL2 - revision: 8b635c0d13
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_ANTITARGET
github-actions / JUnit Test Report
Test Process CNVKIT_ANTITARGET.human - 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-cd2387044731fed43f2a2335fc9acb79.nf` [festering_sammet] DSL2 - revision: a64e289c5a
Nextflow stderr:
Check failure on line 1 in Test Process CNVKIT_BATCH
github-actions / JUnit Test Report
Test Process CNVKIT_BATCH.cnvkit batch tumouronly mode - cram
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-ab1d27684c4099b417741c2bdbb3cac3.nf` [jolly_wilson] DSL2 - revision: 26648234ce
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-ab1d27684c4099b417741c2bdbb3cac3.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/ab1d27684c4099b417741c2bdbb3cac3/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process CNVKIT_REFERENCE
github-actions / JUnit Test Report
Test Process CNVKIT_REFERENCE.human - [fasta, 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-fc0c994df3a2ddaf5353f067300dbe37.nf` [special_heyrovsky] 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
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` [prickly_lichterman] 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
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` [mighty_sinoussi] 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
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` [hopeful_dalembert] DSL2 - revision: de74395a7c
Nextflow stderr:
Check failure on line 1 in Test Process FGBIO_FASTQTOBAM
github-actions / JUnit Test Report
Test Process FGBIO_FASTQTOBAM.homo_sapiens - [fastq1, fastq2] - default
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-f5eacd20d1556d1750c5771b6dc0160.nf` [astonishing_poitras] 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-f5eacd20d1556d1750c5771b6dc0160.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/f5eacd20d1556d1750c5771b6dc0160/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process FGBIO_FASTQTOBAM
github-actions / JUnit Test Report
Test Process FGBIO_FASTQTOBAM.homo_sapiens - [fastq1, fastq2] - custom sample
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-1c22261b493fac4a76f4120326e83446.nf` [desperate_leibniz] 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-1c22261b493fac4a76f4120326e83446.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/1c22261b493fac4a76f4120326e83446/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process FREEBAYES
github-actions / JUnit Test Report
Test Process FREEBAYES.sarscov2 - [ bam, bai, 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-e204b4417e5862c7959e35e50bd61780.nf` [romantic_shaw] DSL2 - revision: d23c72b513
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-e204b4417e5862c7959e35e50bd61780.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/e204b4417e5862c7959e35e50bd61780/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_BASERECALIBRATOR
github-actions / JUnit Test Report
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam - multiple sites
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-416b04d7bd8f043e10869fbccf1ceb6d.nf` [cheeky_goldstine] DSL2 - revision: 39b715024b
[69/71d897] Submitted process > GATK4_BASERECALIBRATOR (test)
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY
github-actions / JUnit Test Report
Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.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-b7f3bb99b7cc55b0ea32e54f131c8e5c.nf` [pedantic_hamilton] DSL2 - revision: 92ef6ec0a5
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram
[6e/18292d] Submitted process > GATK4_ESTIMATELIBRARYCOMPLEXITY (test)
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_HAPLOTYPECALLER
github-actions / JUnit Test Report
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi
Assertion failed:
3 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-1369ef3c6626c54340f532598d7f7596.nf` [awesome_lattes] DSL2 - revision: 5fed09235e
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-1369ef3c6626c54340f532598d7f7596.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/1369ef3c6626c54340f532598d7f7596/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_MUTECT2
github-actions / JUnit Test Report
Test Process GATK4_MUTECT2.generate_pon
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-b39aee658500c245f9392a3430ec4e0b.nf` [cheeky_monod] DSL2 - revision: e273b8ec26
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-b39aee658500c245f9392a3430ec4e0b.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/b39aee658500c245f9392a3430ec4e0b/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process GATK4SPARK_APPLYBQSR
github-actions / JUnit Test Report
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam - 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-89e45f01834626360220afb1d4e2a4aa.nf` [ecstatic_jennings] DSL2 - revision: 33fc4b90d4
[ca/6d92fd] Submitted process > GATK4SPARK_APPLYBQSR (test)
Nextflow stderr:
Check failure on line 1 in Test Process GATK4SPARK_MARKDUPLICATES
github-actions / JUnit Test Report
Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - cram
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-6f96dea42e571478b84ecf81f76385d7.nf` [nauseous_lovelace] 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-6f96dea42e571478b84ecf81f76385d7.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/6f96dea42e571478b84ecf81f76385d7/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process LOFREQ_CALLPARALLEL
github-actions / JUnit Test Report
Test Process LOFREQ_CALLPARALLEL.sarscov2 - bam - bed
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-5f117871e1889c231d0fe09cbcfca03a.nf` [mighty_elion] DSL2 - revision: d8264c2c1e
[52/b5b3fb] Submitted process > LOFREQ_CALLPARALLEL (test)
Nextflow stderr:
Check failure on line 1 in Test Process MANTA_TUMORONLY
github-actions / JUnit Test Report
Test Process MANTA_TUMORONLY.human - cram - bed
Assertion failed:
1 of 5 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-1a3a25f34f203c23d44f9b1f58479f5e.nf` [intergalactic_archimedes] DSL2 - revision: d661e4811c
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram
[6c/f3f2c5] Submitted process > MANTA_TUMORONLY (bed_test)
Nextflow stderr:
Check failure on line 1 in Test Process MOSDEPTH
github-actions / JUnit Test Report
Test Process MOSDEPTH.homo_sapiens - cram, crai, bed
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-ddc27881593e2ba9fc5577a182a6eb27.nf` [pedantic_swanson] DSL2 - revision: ae0b812891
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-ddc27881593e2ba9fc5577a182a6eb27.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/ddc27881593e2ba9fc5577a182a6eb27/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process MOSDEPTH
github-actions / JUnit Test Report
Test Process MOSDEPTH.homo_sapiens - bam, bai, [] - 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-1c548e477f2a518af9ed1868e1819d63.nf` [amazing_ampere] DSL2 - revision: d7cc9c930e
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-1c548e477f2a518af9ed1868e1819d63.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/1c548e477f2a518af9ed1868e1819d63/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process NGSCHECKMATE_NCM
github-actions / JUnit Test Report
Test Process NGSCHECKMATE_NCM.sarscov2 - vcf
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-4a56b6db24002b31b92e82d6a5d3621.nf` [awesome_jones] DSL2 - revision: 3b0773cc8c
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-4a56b6db24002b31b92e82d6a5d3621.nf' at line: 11 or see '/home/runner/work/sarek/sarek/.nf-test/tests/4a56b6db24002b31b92e82d6a5d3621/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process SAMTOOLS_STATS
github-actions / JUnit Test Report
Test Process SAMTOOLS_STATS.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-bd380dd9eb5fb00dc440097b6c801615.nf` [jovial_lovelace] DSL2 - revision: 79d3e6220e
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram
[19/2bf193] Submitted process > SAMTOOLS_STATS (test)
Nextflow stderr: