73 tests run, 38 passed, 0 skipped, 35 failed.
Annotations
Check failure on line 1 in Test Process BCFTOOLS_ANNOTATE
github-actions / JUnit Test Report
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index
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-de7728e7a39c4fb8ed0a28084071d141.nf` [deadly_planck] 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-de7728e7a39c4fb8ed0a28084071d141.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/de7728e7a39c4fb8ed0a28084071d141/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process BCFTOOLS_ANNOTATE
github-actions / JUnit Test Report
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub
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-f4511e0211ba2a7d7ed6468917388ed1.nf` [loving_mercator] DSL2 - revision: a01a43d4bb
Process `BCFTOOLS_ANNOTATE` declares 4 input channels but 2 were specified
-- Check script '/home/runner/work/sarek/sarek/.nf-test-f4511e0211ba2a7d7ed6468917388ed1.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/f4511e0211ba2a7d7ed6468917388ed1/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, true stub
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-5c72b8e967e96cd3fccb9de6842449fb.nf` [cheeky_kowalevski] DSL2 - revision: 804fd5d270
Nextflow stderr:
Check failure on line 1 in Test Process BCFTOOLS_SORT
github-actions / JUnit Test Report
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_csi
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-29fefe56cd022d307d6aab95d45a39bb.nf` [fervent_faggin] DSL2 - revision: be84272338
[be/630c2c] Submitted process > BCFTOOLS_SORT (test)
Nextflow stderr:
Check failure on line 1 in Test Process BCFTOOLS_SORT
github-actions / JUnit Test Report
Test Process BCFTOOLS_SORT.sarscov2 - vcf_gz_index_tbi - 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-78cdaf6ccf842e2dfae5d97f5baa66c1.nf` [sleepy_fermi] DSL2 - revision: be84272338
[20/3f9bb9] Submitted process > BCFTOOLS_SORT (test)
Nextflow stderr:
Check failure on line 1 in Test Process BWA_MEM
github-actions / JUnit Test Report
Test Process BWA_MEM.Paired-End
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-b09a99ea6f2d58dc862296051abad10d.nf` [drunk_lamarck] DSL2 - revision: 4b3bc9a0de
[88/50aa80] Submitted process > BWA_INDEX (genome.fasta)
[ab/e16b41] Submitted process > BWA_MEM (test)
Nextflow stderr:
Check failure on line 1 in Test Process BWAMEM2_INDEX
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` [voluminous_tuckerman] 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
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` [admiring_murdock] 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
github-actions / JUnit Test Report
Test Process CNVKIT_BATCH.cnvkit batch wgs - 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-292f1ec56a73660a63c415c9108ee105.nf` [thirsty_davinci] DSL2 - revision: 64af3e2e92
Nextflow stderr:
Check failure on line 1 in Test Process CNVKIT_BATCH
github-actions / JUnit Test Report
Test Process CNVKIT_BATCH.cnvkit batch germline hybrid mode - 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-3343e7f1553c6a650a18ad130d6c54f7.nf` [furious_nobel] DSL2 - revision: eba8b00192
Nextflow stderr:
Check failure on line 1 in Test Process CONTROLFREEC_ASSESSSIGNIFICANCE
github-actions / JUnit Test Report
Test Process CONTROLFREEC_ASSESSSIGNIFICANCE.human - freec_ratio
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-2a65617fc083728b5273aa1dd510a2f.nf` [loving_torvalds] DSL2 - revision: 66b9d3a038
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz
[bc/2dcc1e] Submitted process > UNTAR (chromosomes.tar.gz)
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz
[ce/6491e6] Submitted process > CONTROLFREEC_FREEC (test)
[ae/bdedcd] Submitted process > CONTROLFREEC_ASSESSSIGNIFICANCE (test)
Nextflow stderr:
Check failure on line 1 in Test Process DEEPVARIANT_RUNDEEPVARIANT
github-actions / JUnit Test Report
Test Process DEEPVARIANT_RUNDEEPVARIANT.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-d6f7b4e5d8fd9a85eac6d8da2a354697.nf` [peaceful_kalman] DSL2 - revision: 93781fac4c
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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-93a48027b942baa9df4a12392a55f22d.nf` [condescending_panini] 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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-a5b1269efe68ee0986c48e1cf1b9b4ac.nf` [tiny_boyd] 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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-4d1266b20b946118eb1361cd789a8a13.nf` [amazing_bhabha] DSL2 - revision: 3548fcde48
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:
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-e204b4417e5862c7959e35e50bd61780.nf` [soggy_kalman] DSL2 - revision: 12ba401587
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` [soggy_hoover] DSL2 - revision: 39b715024b
[aa/e9b7b6] 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` [high_bartik] DSL2 - revision: 92ef6ec0a5
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram
[fe/1f043c] Submitted process > GATK4_ESTIMATELIBRARYCOMPLEXITY (test)
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_GENOMICSDBIMPORT
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` [focused_borg] DSL2 - revision: ade31c482b
[d4/8f7ad4] Submitted process > UNTAR (test_genomicsdb.tar.gz)
[72/36dbdb] Submitted process > GATK4_GENOMICSDBIMPORT (test)
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_GENOTYPEGVCFS
github-actions / JUnit Test Report
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []
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-1466abd8691373f84f8940ad07079f17.nf` [special_gauss] DSL2 - revision: 5f6ffbdc12
[77/498674] Submitted process > UNTAR (test_genomicsdb.tar.gz)
[40/ac99fa] Submitted process > GATK4_GENOTYPEGVCFS (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, dragstr_model] - 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-d3b0f8888e8ff7fd9f3d562dc0f2d2ff.nf` [grave_wiles] DSL2 - revision: 4524132e17
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` [happy_stone] DSL2 - revision: 33fc4b90d4
[8d/53c5ee] 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` [boring_kay] 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` [infallible_williams] DSL2 - revision: d8264c2c1e
[1e/731f54] 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` [loving_bassi] DSL2 - revision: d661e4811c
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram
[7d/fd6c1d] Submitted process > MANTA_TUMORONLY (bed_test)
Nextflow stderr: