72 tests run, 35 passed, 0 skipped, 37 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_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-5205203429b04daa213d34d362219af3.nf` [sick_noether] 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-5205203429b04daa213d34d362219af3.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/5205203429b04daa213d34d362219af3/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_tbi - 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-f8ea7c8fb29eedc9a9c837e0ed3ee91a.nf` [elegant_keller] DSL2 - revision: a01a43d4bb
Process `BCFTOOLS_ANNOTATE` declares 4 input channels but 2 were specified
-- Check script '/home/runner/work/sarek/sarek/.nf-test-f8ea7c8fb29eedc9a9c837e0ed3ee91a.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/f8ea7c8fb29eedc9a9c837e0ed3ee91a/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:
4 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` [ridiculous_murdock] DSL2 - revision: dbb3271155
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:
4 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` [loving_newton] DSL2 - revision: 9f99721e09
Nextflow stderr:
Check failure on line 1 in Test Process BCFTOOLS_SORT
github-actions / JUnit Test Report
Test Process BCFTOOLS_SORT.sarscov2 - vcf - 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-44e4658d575ca4d2b322c5468e5b2101.nf` [distracted_lorenz] DSL2 - revision: be84272338
[63/b2aff8] 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 - no 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-ae8f3f6e323f3a92659053719fda7b38.nf` [infallible_easley] DSL2 - revision: cb8f8c2ca8
[aa/a71471] Submitted process > BWA_INDEX (genome.fasta)
[a3/21040a] Submitted process > BWA_MEM (test)
Nextflow stderr:
Check failure on line 1 in Test Process BWAMEM2_MEM
github-actions / JUnit Test Report
Test Process BWAMEM2_MEM.sarscov2 - fastq, index, 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-bcc5375c772b31c142ac8958729bac4d.nf` [ridiculous_roentgen] DSL2 - revision: 9ec3a133d0
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
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-98b23e12ef50d69147dc338977202830.nf` [lonely_meitner] 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 - 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-5f896e0cc48445bb4d69274fea79eafd.nf` [nasty_snyder] DSL2 - revision: fc4f01d0a9
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam
Nextflow stderr:
Check failure on line 1 in Test Process CNVKIT_BATCH
github-actions / JUnit Test Report
Test Process CNVKIT_BATCH.cnvkit batch - 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-c0b389dfc4bbaa4247bfcc8937e4176e.nf` [fervent_wilson] DSL2 - revision: d080a1761d
Nextflow stderr:
Check failure on line 1 in Test Process CNVKIT_GENEMETRICS
github-actions / JUnit Test Report
Test Process CNVKIT_GENEMETRICS.test-cnvkit-genemetrics-without-cns
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-20a793b30e049bd7d222138b2a04fecf.nf` [golden_kirch] DSL2 - revision: e68a19f0db
Nextflow stderr:
Check failure on line 1 in Test Process DEEPVARIANT_RUNDEEPVARIANT
github-actions / JUnit Test Report
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_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-8048e98d0283bd73f99a7c91b716e256.nf` [festering_moriondo] DSL2 - revision: aa1f5d0263
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
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-6e218af819229bc0e002268668aaea8f.nf` [trusting_keller] 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_DOWNLOAD
github-actions / JUnit Test Report
Test Process ENSEMBLVEP_DOWNLOAD.celegans - 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-14ead4ea0d7ecbb2734396b10c682029.nf` [happy_wescoff] DSL2 - revision: 450f7067f5
Nextflow stderr:
Check failure on line 1 in Test Process FASTP
github-actions / JUnit Test Report
Test Process FASTP.test_fastp_paired_end
Assertion failed:
2 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-8711bc8a4f139041763bf1c226715a23.nf` [high_lamarck] DSL2 - revision: 9cddfe4326
[29/6561cc] Submitted process > FASTP (test)
Nextflow stderr:
Check failure on line 1 in Test Process FASTP
github-actions / JUnit Test Report
Test Process FASTP.test_fastp_paired_end_merged_adapterlist
Assertion failed:
1 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-a5cdf7a2217ae0d6290ef653bc07b9cc.nf` [goofy_brown] DSL2 - revision: 120969a847
[bb/0c17c0] Submitted process > FASTP (test)
Nextflow stderr:
Check failure on line 1 in Test Process FGBIO_CALLMOLECULARCONSENSUSREADS
github-actions / JUnit Test Report
Test Process FGBIO_CALLMOLECULARCONSENSUSREADS.homo_sapiens - 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-47cedca04cdabf8e73f1dc4f550ecc83.nf` [grave_faggin] DSL2 - revision: 797542d3d3
ERROR ~ No such file or directory: Can't find a matching module file for include: /home/runner/work/sarek/sarek/modules/nf-core/fgbio/callmolecularconsensusreads/tests/../../sortbam/main.nf
-- Check script '/home/runner/work/sarek/sarek/.nf-test-47cedca04cdabf8e73f1dc4f550ecc83.nf' at line: 11 or see '/home/runner/work/sarek/sarek/.nf-test/tests/47cedca04cdabf8e73f1dc4f550ecc83/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 ] - 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-c1f0c01cc4505636ab01fbf576bcb828.nf` [cranky_bose] DSL2 - revision: 9bbf7bf8f4
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_APPLYBQSR
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` [festering_varahamihira] DSL2 - revision: e17171bd45
[e0/c2ba70] Submitted process > GATK4_APPLYBQSR (test)
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_BASERECALIBRATOR
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` [awesome_lamarr] DSL2 - revision: 6513c12b9c
[22/efe2d9] Submitted process > GATK4_BASERECALIBRATOR (test)
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_GATHERBQSRREPORTS
github-actions / JUnit Test Report
Test Process GATK4_GATHERBQSRREPORTS.test-gatk4-gatherbqsrreports-multiple
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-777d06bf58c12c4e5bffe73c682ce47d.nf` [sleepy_mayer] DSL2 - revision: 7f70333bc6
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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-801f5900031a4a8b8737898b6f9ca697.nf` [fabulous_legentil] DSL2 - revision: cebaf8f854
[9a/9410fe] 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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-b80a86a92d2e14b540cb3f0461e8f4a1.nf` [evil_ampere] DSL2 - revision: 2b996036be
[94/fedc8b] Submitted process > UNTAR (test_genomicsdb.tar.gz)
[16/09ea0e] 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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-f3e35d13d24e811920c8f2f6742f3efe.nf` [jovial_lichterman] 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 23.04.0
Launching `/home/runner/work/sarek/sarek/.nf-test-c39d9aa5d415aa6f1dd8a64487cbdabf.nf` [jovial_pike] 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: