Add nf-test sharding CI #8
55 tests run, 30 passed, 0 skipped, 25 failed.
Annotations
Check failure on line 1 in Test Process BCFTOOLS_CONCAT
github-actions / JUnit Test Report
Test Process BCFTOOLS_CONCAT.sarscov2 - [[vcf1, vcf2], []]
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-f55c0d584b19b34ab25e55dd798cf1f9.nf` [irreverent_easley] DSL2 - revision: 0d2d3ebc12
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 'homo_sapiens' on null object
-- Check script '/home/runner/work/sarek/sarek/.nf-test-f55c0d584b19b34ab25e55dd798cf1f9.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/f55c0d584b19b34ab25e55dd798cf1f9/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:
6 of 6 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-5c72b8e967e96cd3fccb9de6842449fb.nf` [jolly_boltzmann] DSL2 - revision: 6443073f16
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-5c72b8e967e96cd3fccb9de6842449fb.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/5c72b8e967e96cd3fccb9de6842449fb/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 - fastq, index, fasta, false
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-ed4be5f8101e3149a8f921495eb18bd1.nf` [naughty_mcnulty] DSL2 - revision: c17c9c620e
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 - 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-8b9fbda3a86982967a817867f87058c9.nf` [small_austin] DSL2 - revision: c2526d6d5a
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-8b9fbda3a86982967a817867f87058c9.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/8b9fbda3a86982967a817867f87058c9/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 pon mode - bam
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-996f7ae2066691a85efc1f62237ee0a0.nf` [lonely_gautier] DSL2 - revision: b124a0e16c
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-996f7ae2066691a85efc1f62237ee0a0.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/996f7ae2066691a85efc1f62237ee0a0/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process DEEPVARIANT
github-actions / JUnit Test Report
Test Process DEEPVARIANT.homo_sapiens - [cram, crai, genome_bed] - fasta - fai
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-d200f1e5bf86cb0d2c8710b188cdb330.nf` [confident_golick] DSL2 - revision: b7dbe1fd21
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 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-6e218af819229bc0e002268668aaea8f.nf` [berserk_sinoussi] 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 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-14ead4ea0d7ecbb2734396b10c682029.nf` [nauseous_ramanujan] DSL2 - revision: d0a45e4f8b
Nextflow stderr:
Check failure on line 1 in Test Process FASTP
github-actions / JUnit Test Report
Test Process FASTP.test_fastp_single_end_trim_fail
Assertion failed:
1 of 7 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-9a576f8326ef1386c3e350f64c0c98c5.nf` [goofy_thompson] DSL2 - revision: 59ce5685b7
[30/37e066] Submitted process > FASTP (test)
WARN: Process `FASTP` publishDir path contains a variable with a null value
Nextflow stderr:
Check failure on line 1 in Test Process FGBIO_FASTQTOBAM
github-actions / JUnit Test Report
Test Process FGBIO_FASTQTOBAM.homo_sapiens - fastq1
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-68a423c407cab84518e92429dbdb2f3f.nf` [backstabbing_curran] DSL2 - revision: 46d8ca39ec
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-68a423c407cab84518e92429dbdb2f3f.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/68a423c407cab84518e92429dbdb2f3f/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, bed ] - fasta - fai
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-9aae176295e07f80bcdecbc29382a111.nf` [evil_goldberg] DSL2 - revision: 04d30cf54b
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-9aae176295e07f80bcdecbc29382a111.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/9aae176295e07f80bcdecbc29382a111/meta/nextflow.log' file for more details
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 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-a05a77b4cd5de4b36b6ff13553d35e1c.nf` [curious_einstein] DSL2 - revision: a56223f979
[5a/15cfc7] 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 24.08.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-3fbe2566272570dc500819f3ce7b7ff9.nf` [chaotic_picasso] DSL2 - revision: bb48ff4584
[3f/18f79d] 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_HAPLOTYPECALLER
github-actions / JUnit Test Report
Test Process GATK4_HAPLOTYPECALLER.homo_sapiens - [bam, bai] - fasta - fai - dict
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-f3e35d13d24e811920c8f2f6742f3efe.nf` [elegant_euler] DSL2 - revision: 4be2d5efce
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-f3e35d13d24e811920c8f2f6742f3efe.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/f3e35d13d24e811920c8f2f6742f3efe/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_single
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-7481f7eeda51c99c1aa0d2b3628f71ff.nf` [disturbed_feynman] DSL2 - revision: 6fac076e73
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-7481f7eeda51c99c1aa0d2b3628f71ff.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/7481f7eeda51c99c1aa0d2b3628f71ff/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 - bam
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-c89e246cda82587cacddd788d34b43fb.nf` [astonishing_bose] DSL2 - revision: 753a2d256e
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-c89e246cda82587cacddd788d34b43fb.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/c89e246cda82587cacddd788d34b43fb/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process GATK4SPARK_MARKDUPLICATES
github-actions / JUnit Test Report
Test Process GATK4SPARK_MARKDUPLICATES.homo_sapiens - bam - multiple
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-734baa670beda97ecfabe2c8128e29ea.nf` [lonely_thompson] 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-734baa670beda97ecfabe2c8128e29ea.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/734baa670beda97ecfabe2c8128e29ea/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, bed
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-c2423a8b537d45b97e5a929140ee419e.nf` [exotic_hilbert] DSL2 - revision: d7cc9c930e
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-c2423a8b537d45b97e5a929140ee419e.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/c2423a8b537d45b97e5a929140ee419e/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, bed - thresholds
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-9d435a0ca7acbc55e4bd514b5656ffbb.nf` [elegant_magritte] DSL2 - revision: d7cc9c930e
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-9d435a0ca7acbc55e4bd514b5656ffbb.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/9d435a0ca7acbc55e4bd514b5656ffbb/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process SAMBLASTER
github-actions / JUnit Test Report
Test Process SAMBLASTER.homo_sapiens-test_paired_end_umi_unsorted_bam
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-7c48e33d286b47b5098e1589a8daf83d.nf` [fervent_moriondo] DSL2 - revision: 2d99b1e7d3
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-7c48e33d286b47b5098e1589a8daf83d.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/7c48e33d286b47b5098e1589a8daf83d/meta/nextflow.log' file for more details
Nextflow stderr:
Check failure on line 1 in Test Process SAMTOOLS_MPILEUP
github-actions / JUnit Test Report
Test Process SAMTOOLS_MPILEUP.bam_bed_fasta
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-a8ef959546fb06c7433384000aa2fec2.nf` [desperate_galileo] DSL2 - revision: e314ee1698
Nextflow stderr:
Check failure on line 1 in Test Process SNPEFF_DOWNLOAD
github-actions / JUnit Test Report
Test Process SNPEFF_DOWNLOAD.test-snpeff-download-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-6c25880801a432296ef801e532e21b84.nf` [desperate_boyd] DSL2 - revision: 629db28a71
Nextflow stderr:
Check failure on line 1 in Test Process TABIX_BGZIPTABIX
github-actions / JUnit Test Report
Test Process TABIX_BGZIPTABIX.sarscov2_bed_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-685a05aae81f09694897bc527ed8aeaa.nf` [happy_kalam] DSL2 - revision: 5ea3f2c72a
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-685a05aae81f09694897bc527ed8aeaa.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/685a05aae81f09694897bc527ed8aeaa/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_vcf_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-4821466480f316d62414176e53a0a880.nf` [spontaneous_wescoff] DSL2 - revision: 86bc1a799e
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-4821466480f316d62414176e53a0a880.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/4821466480f316d62414176e53a0a880/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.human - cram - 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-b467714618fbda0c5b6cc7342162e6fb.nf` [goofy_almeida] DSL2 - revision: c1b3189385
[98/bac671] Submitted process > BWA_INDEX (genome.fasta)
WARN: Process `BWA_INDEX` publishDir path contains a variable with a null value
Nextflow stderr: