Add nf-test sharding CI #24
74 tests run, 38 passed, 0 skipped, 36 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_output
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-dee4edbd680ab6c99118d7e7e772f8f6.nf` [sick_mayer] 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-dee4edbd680ab6c99118d7e7e772f8f6.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/dee4edbd680ab6c99118d7e7e772f8f6/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, [], annotation, annotation_tbi], header - bcf_output
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-190fe4ec4971a87d855485c07279520.nf` [curious_panini] DSL2 - revision: d4d8121b0d
Process `BCFTOOLS_ANNOTATE` declares 4 input channels but 2 were specified
-- Check script '/home/runner/work/sarek/sarek/.nf-test-190fe4ec4971a87d855485c07279520.nf' at line: 47 or see '/home/runner/work/sarek/sarek/.nf-test/tests/190fe4ec4971a87d855485c07279520/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:
4 of 5 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-e510fb920fc9c79e1710c14d24b3204e.nf` [tiny_lagrange] DSL2 - revision: dbb3271155
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:
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-ae16dc3311a6e4226132f2a238ff1409.nf` [jovial_ramanujan] DSL2 - revision: be84272338
[02/9c0229] 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 - 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-5a46b0681ee420d2227042c330270071.nf` [mad_wegener] DSL2 - revision: be84272338
[76/586f98] 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.Single-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-d67e0b05ee8c8f813b90b3e24783c2ed.nf` [insane_lamarck] DSL2 - revision: b604a0111a
[63/640c6e] Submitted process > BWA_INDEX (genome.fasta)
WARN: Process `BWA_INDEX` publishDir path contains a variable with a null value
[da/a77e9d] 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_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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-7136dedfcfcc8e5e0e35f11b11b79c8.nf` [gigantic_torricelli] DSL2 - revision: 0d8fdd03d0
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-cd2387044731fed43f2a2335fc9acb79.nf` [high_escher] 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:
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-ab1d27684c4099b417741c2bdbb3cac3.nf` [kickass_brattain] DSL2 - revision: 0ff543f9be
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram
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:
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-fc0c994df3a2ddaf5353f067300dbe37.nf` [peaceful_wozniak] 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 DEEPVARIANT_RUNDEEPVARIANT
github-actions / JUnit Test Report
Test Process DEEPVARIANT_RUNDEEPVARIANT.homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_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-f899d996b10767aaad51156eccbc2891.nf` [distracted_angela] DSL2 - revision: 6205220fab
Nextflow stderr:
Check failure on line 1 in Test Process DRAGMAP_ALIGN
github-actions / JUnit Test Report
Test Process DRAGMAP_ALIGN.homo_sapiens - [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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-db0364ca3785deddf5b057df6e81d750.nf` [cheeky_mayer] DSL2 - revision: b4eeb474c0
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 - 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-9dd1140166c0d130158c1c556838d52d.nf` [elegant_heyrovsky] DSL2 - revision: 450f7067f5
Nextflow stderr:
Check failure on line 1 in Test Process FASTP
github-actions / JUnit Test Report
Test Process FASTP.test_fastp_single_end_qc_only
Assertion failed:
1 of 4 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-af1f771742fce71c41840c430819ab53.nf` [wise_faraday] DSL2 - revision: d18ac51e92
[b3/e2fc20] Submitted process > FASTP (test)
WARN: Process `FASTP` publishDir path contains a variable with a null value
WARN: Process `FASTP` publishDir path contains a variable with a null value
Nextflow stderr:
Check failure on line 1 in Test Process FREEBAYES
github-actions / JUnit Test Report
Test Process FREEBAYES.sarscov2 - [ bam, bai, bed ] - 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-9aae176295e07f80bcdecbc29382a111.nf` [stoic_gauss] DSL2 - revision: 4231546996
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_APPLYBQSR
github-actions / JUnit Test Report
Test Process GATK4_APPLYBQSR.sarscov2 - bam - intervals
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-a05a77b4cd5de4b36b6ff13553d35e1c.nf` [trusting_mendel] DSL2 - revision: a56223f979
[ff/d95a29] 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 - 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-f9fa66b120172469cb1a65015b64dd63.nf` [mighty_lamarr] DSL2 - revision: 4948fc9022
[3a/8433c3] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-ecff9ee5b652c6082f77cf4286fefb83.nf` [extravagant_newton] DSL2 - revision: b5ad5c616e
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam
[34/74415b] 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_GATHERBQSRREPORTS
github-actions / JUnit Test Report
Test Process GATK4_GATHERBQSRREPORTS.test-gatk4-gatherbqsrreports
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-c3489e005da2acc3de8a2478072d22f5.nf` [curious_mendel] DSL2 - revision: 121728c0b1
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-6295e742960e2235da53319c04fc7f8e.nf` [extravagant_aryabhata] DSL2 - revision: ade31c482b
[5c/8c7dff] Submitted process > UNTAR (test_genomicsdb.tar.gz)
WARN: Process `UNTAR` publishDir path contains a variable with a null value
[fd/3a4858] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-1466abd8691373f84f8940ad07079f17.nf` [adoring_torricelli] DSL2 - revision: 5f6ffbdc12
[41/76b9ce] Submitted process > UNTAR (test_genomicsdb.tar.gz)
[01/697e76] Submitted process > GATK4_GENOTYPEGVCFS (test)
WARN: Process `UNTAR` 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:
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-d3b0f8888e8ff7fd9f3d562dc0f2d2ff.nf` [berserk_pesquet] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-89e45f01834626360220afb1d4e2a4aa.nf` [nasty_volhard] DSL2 - revision: 33fc4b90d4
[6c/51e1f4] Submitted process > GATK4SPARK_APPLYBQSR (test)
WARN: Process `GATK4SPARK_APPLYBQSR` publishDir path contains a variable with a null value
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-6f96dea42e571478b84ecf81f76385d7.nf` [special_yonath] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-5f117871e1889c231d0fe09cbcfca03a.nf` [pensive_fermat] DSL2 - revision: d8264c2c1e
[1f/952a8f] Submitted process > LOFREQ_CALLPARALLEL (test)
WARN: Process `LOFREQ_CALLPARALLEL` publishDir path contains a variable with a null value
Nextflow stderr: