Merge branch 'dev' into fresh-nf-test
73 tests run, 39 passed, 0 skipped, 34 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-de7728e7a39c4fb8ed0a28084071d141.nf` [voluminous_sanger] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f4511e0211ba2a7d7ed6468917388ed1.nf` [big_banach] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-5c72b8e967e96cd3fccb9de6842449fb.nf` [cranky_dalembert] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-29fefe56cd022d307d6aab95d45a39bb.nf` [sick_yonath] DSL2 - revision: be84272338
[0b/1a9868] Submitted process > BCFTOOLS_SORT (test)
WARN: Process `BCFTOOLS_SORT` publishDir path contains a variable with a null value
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-78cdaf6ccf842e2dfae5d97f5baa66c1.nf` [irreverent_woese] DSL2 - revision: be84272338
[10/14cef0] Submitted process > BCFTOOLS_SORT (test)
WARN: Process `BCFTOOLS_SORT` publishDir path contains a variable with a null value
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-b09a99ea6f2d58dc862296051abad10d.nf` [modest_payne] DSL2 - revision: 4b3bc9a0de
[e7/126c30] Submitted process > BWA_INDEX (genome.fasta)
WARN: Process `BWA_INDEX` publishDir path contains a variable with a null value
[cd/2e9154] Submitted process > BWA_MEM (test)
WARN: Process `BWA_MEM` publishDir path contains a variable with a null value
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-cee0b72aac42f68c14744e38cad163a4.nf` [extravagant_noyce] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-4a9ac93358a712ca91dfe1d0ae278d0d.nf` [awesome_wescoff] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-292f1ec56a73660a63c415c9108ee105.nf` [maniac_galileo] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-3343e7f1553c6a650a18ad130d6c54f7.nf` [hopeful_ampere] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-2a65617fc083728b5273aa1dd510a2f.nf` [fervent_ampere] DSL2 - revision: 66b9d3a038
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz
[6f/56a8b2] Submitted process > UNTAR (chromosomes.tar.gz)
WARN: Process `UNTAR` publishDir path contains a variable with a null value
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz
[73/717d6a] Submitted process > CONTROLFREEC_FREEC (test)
WARN: Process `CONTROLFREEC_FREEC` publishDir path contains a variable with a null value
[06/00db73] Submitted process > CONTROLFREEC_ASSESSSIGNIFICANCE (test)
WARN: Process `CONTROLFREEC_ASSESSSIGNIFICANCE` publishDir path contains a variable with a null value
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-d6f7b4e5d8fd9a85eac6d8da2a354697.nf` [confident_kimura] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-93a48027b942baa9df4a12392a55f22d.nf` [ecstatic_saha] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-a5b1269efe68ee0986c48e1cf1b9b4ac.nf` [deadly_blackwell] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-4d1266b20b946118eb1361cd789a8a13.nf` [sad_bohr] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-e204b4417e5862c7959e35e50bd61780.nf` [irreverent_borg] DSL2 - revision: 12ba401587
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_APPLYBQSR
github-actions / JUnit Test Report
Test Process GATK4_APPLYBQSR.sarscov2 - cram - stub
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-d1408209f6005b1b837b91dce600cbca.nf` [loving_williams] DSL2 - revision: 675f8b19b6
[a3/364e2b] Submitted process > GATK4_APPLYBQSR (test)
WARN: Process `GATK4_APPLYBQSR` publishDir path contains a variable with a null value
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_BASERECALIBRATOR
github-actions / JUnit Test Report
Test Process GATK4_BASERECALIBRATOR.sarscov2 - bam
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-3fbe2566272570dc500819f3ce7b7ff9.nf` [distracted_rosalind] DSL2 - revision: bb48ff4584
[99/fc4881] 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_GENOMICSDBIMPORT
github-actions / JUnit Test Report
Test Process GATK4_GENOMICSDBIMPORT.test_gatk4_genomicsdbimport_stub
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-801f5900031a4a8b8737898b6f9ca697.nf` [cheesy_montalcini] DSL2 - revision: cebaf8f854
[33/5cb046] 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 - [gendb, bed, [], []], fasta, fai, dict, [], []
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-b80a86a92d2e14b540cb3f0461e8f4a1.nf` [intergalactic_bernard] DSL2 - revision: 2b996036be
[99/5d6ca6] Submitted process > UNTAR (test_genomicsdb.tar.gz)
WARN: Process `UNTAR` publishDir path contains a variable with a null value
[f5/2cc487] 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 - [bam, bai] - fasta - fai - dict
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f3e35d13d24e811920c8f2f6742f3efe.nf` [intergalactic_dijkstra] DSL2 - revision: b919bc73a4
Nextflow stderr:
Check failure on line 1 in Test Process GATK4SPARK_MARKDUPLICATES
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-c39d9aa5d415aa6f1dd8a64487cbdabf.nf` [suspicious_swirles] 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
github-actions / JUnit Test Report
Test Process MOSDEPTH.homo_sapiens - bam, bai, []
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-5e46c99d36b094824d7f084d29773397.nf` [compassionate_heyrovsky] DSL2 - revision: ecf3b8da18
[13/c247a4] Submitted process > MOSDEPTH (test)
WARN: Process `MOSDEPTH` publishDir path contains a variable with a null value
Nextflow stderr:
Check failure on line 1 in Test Process MOSDEPTH
github-actions / JUnit Test Report
Test Process MOSDEPTH.homo_sapiens - bam, bai, [] - quantized
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-c01a7d21d5a293f5f254966cbd89a425.nf` [tender_mahavira] DSL2 - revision: ecf3b8da18
[fb/497e63] Submitted process > MOSDEPTH (test)
WARN: Process `MOSDEPTH` publishDir path contains a variable with a null value
Nextflow stderr:
Check failure on line 1 in Test Process MSISENSORPRO_SCAN
github-actions / JUnit Test Report
Test Process MSISENSORPRO_SCAN.test-msisensorpro-scan-stub
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-6625f725e6644aaa1819f37eaff90b9d.nf` [lonely_goldstine] DSL2 - revision: abf84489a3
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta
Nextflow stderr: