Add nf-test sharding CI #8
56 tests run, 33 passed, 0 skipped, 23 failed.
Annotations
Check failure on line 1 in Test Process BCFTOOLS_ANNOTATE
github-actions / JUnit Test Report
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, vcf2, tbi2, []] - stub
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-75158ba71f30d7255a76f3fa959a57ee.nf` [cheeky_brattain] DSL2 - revision: ea9b4f0ae5
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-75158ba71f30d7255a76f3fa959a57ee.nf' at line: 33 or see '/home/runner/work/sarek/sarek/.nf-test/tests/75158ba71f30d7255a76f3fa959a57ee/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 stub
Assertion failed:
5 of 5 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-e510fb920fc9c79e1710c14d24b3204e.nf` [elegant_hypatia] 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-e510fb920fc9c79e1710c14d24b3204e.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/e510fb920fc9c79e1710c14d24b3204e/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process BCFTOOLS_SORT
github-actions / JUnit Test Report
Test Process BCFTOOLS_SORT.sarscov2 - vcf
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-ae16dc3311a6e4226132f2a238ff1409.nf` [exotic_cuvier] 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-ae16dc3311a6e4226132f2a238ff1409.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/ae16dc3311a6e4226132f2a238ff1409/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, true
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-52fa0d2217318220d5a3490f900f5fa4.nf` [loquacious_lalande] 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
github-actions / JUnit Test Report
Test Process CNVKIT_BATCH.cnvkit batch hybrid mode - bam
java.lang.RuntimeException: Process has no output channels. process.out can not be used.
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-fc438db575bababb4a6f66ac343408c6.nf` [focused_wiles] 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-fc438db575bababb4a6f66ac343408c6.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/fc438db575bababb4a6f66ac343408c6/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process CNVKIT_BATCH
github-actions / JUnit Test Report
Test Process CNVKIT_BATCH.cnvkit batch germline mode - cram
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-3c695a64203190e2ed69ae6bdc34d119.nf` [nice_leakey] DSL2 - revision: 9d352bb8dc
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-3c695a64203190e2ed69ae6bdc34d119.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/3c695a64203190e2ed69ae6bdc34d119/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] - stub
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-ff87ec3fed425dabc30eb6cc831f4c13.nf` [compassionate_koch] 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, true
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-93a48027b942baa9df4a12392a55f22d.nf` [disturbed_goldberg] DSL2 - revision: 63a011dd85
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
github-actions / JUnit Test Report
Test Process DRAGMAP_HASHTABLE.sarscov2 - fasta
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-a5b1269efe68ee0986c48e1cf1b9b4ac.nf` [distraught_curie] 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 ENSEMBLVEP_VEP
github-actions / JUnit Test Report
Test Process ENSEMBLVEP_VEP.test_ensemblvep_vep_fasta_tab_gz
Assertion failed:
2 of 3 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-4d1266b20b946118eb1361cd789a8a13.nf` [awesome_cajal] 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] - cram
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-36c0e5e4547c42f19db1c0ba0b6e0b36.nf` [maniac_moriondo] 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-36c0e5e4547c42f19db1c0ba0b6e0b36.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/36c0e5e4547c42f19db1c0ba0b6e0b36/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] - stub
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-8584641ed3b59602c75d613666347a8.nf` [hungry_gates] 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-8584641ed3b59602c75d613666347a8.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/8584641ed3b59602c75d613666347a8/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 - [ cram, crai, cram, crai, bed ] - fasta - fai
Assertion failed:
4 of 4 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-b63773b2e77ac99761d31388d20d5850.nf` [crazy_kimura] DSL2 - revision: 2fdf1699ab
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-b63773b2e77ac99761d31388d20d5850.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/b63773b2e77ac99761d31388d20d5850/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 - stub
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f9fa66b120172469cb1a65015b64dd63.nf` [nostalgic_jones] DSL2 - revision: 4948fc9022
[61/004f78] 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
github-actions / JUnit Test Report
Test Process GATK4_ESTIMATELIBRARYCOMPLEXITY.sarscov2 - bam - stub
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-ecff9ee5b652c6082f77cf4286fefb83.nf` [condescending_khorana] DSL2 - revision: b5ad5c616e
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam
[a4/75fc12] 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_HAPLOTYPECALLER
github-actions / JUnit Test Report
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [cram, crai, dragstr_model] - 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 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-d3b0f8888e8ff7fd9f3d562dc0f2d2ff.nf` [elegant_poisson] DSL2 - revision: b5575db474
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-d3b0f8888e8ff7fd9f3d562dc0f2d2ff.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/d3b0f8888e8ff7fd9f3d562dc0f2d2ff/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.tumor_normal_pair
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-63d67a5bea335f97081be5d90a417151.nf` [spontaneous_easley] 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-63d67a5bea335f97081be5d90a417151.nf' at line: 39 or see '/home/runner/work/sarek/sarek/.nf-test/tests/63d67a5bea335f97081be5d90a417151/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.mitochondria
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-9a138e169e98eb2e333ce4b2276cd889.nf` [gigantic_chandrasekhar] DSL2 - revision: a10cc1b720
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-9a138e169e98eb2e333ce4b2276cd889.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/9a138e169e98eb2e333ce4b2276cd889/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 - cram
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-76a0510efed4985368a5c2abed8da308.nf` [astonishing_hoover] DSL2 - revision: 0470a34d82
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-76a0510efed4985368a5c2abed8da308.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/76a0510efed4985368a5c2abed8da308/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, [] - window
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-4fb5cdcb3ff20c24a9c710f12ca52ee.nf` [insane_mandelbrot] 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-4fb5cdcb3ff20c24a9c710f12ca52ee.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/4fb5cdcb3ff20c24a9c710f12ca52ee/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 - bam - stub
Assertion failed:
2 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-21599b4b6e50dc038c0ca7d130cdc0e4.nf` [mighty_coulomb] DSL2 - revision: c3088b9bf7
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-21599b4b6e50dc038c0ca7d130cdc0e4.nf' at line: 11 or see '/home/runner/work/sarek/sarek/.nf-test/tests/21599b4b6e50dc038c0ca7d130cdc0e4/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process TABIX_TABIX
github-actions / JUnit Test Report
Test Process TABIX_TABIX.sarscov2_bedgz_tbi
Assertion failed:
3 of 3 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-e176c6c343b630e6435421ce4d08ad01.nf` [soggy_engelbart] DSL2 - revision: e8fb3981ad
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-e176c6c343b630e6435421ce4d08ad01.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/e176c6c343b630e6435421ce4d08ad01/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process TIDDIT_SV
github-actions / JUnit Test Report
Test Process TIDDIT_SV.sarscov2 - bam - bwa
Assertion failed:
3 of 4 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-d3c9b43d9c3b67e9b96c37d01e546cc.nf` [disturbed_wright] DSL2 - revision: 5afd7b1ce6
[b2/8ccc0d] Submitted process > BWA_INDEX (genome.fasta)
WARN: Process `BWA_INDEX` publishDir path contains a variable with a null value
Nextflow stderr: