Add nf-test sharding CI #18
72 tests run, 38 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_csi
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-b585981dd3b0690fed7881e81b047773.nf` [trusting_picasso] 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-b585981dd3b0690fed7881e81b047773.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/b585981dd3b0690fed7881e81b047773/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_csi - 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-f2f1b70c46365389c1af72aaa239d04b.nf` [high_chandrasekhar] DSL2 - revision: a01a43d4bb
Process `BCFTOOLS_ANNOTATE` declares 4 input channels but 2 were specified
-- Check script '/home/runner/work/sarek/sarek/.nf-test-f2f1b70c46365389c1af72aaa239d04b.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/f2f1b70c46365389c1af72aaa239d04b/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, bed], fasta, false
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-f3a09604dc6e16eeca9e34b021a2130f.nf` [stupefied_montalcini] 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_gz_index_tbi
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-a92ae67312258e3ab00345cbfad5f80e.nf` [curious_lamarr] DSL2 - revision: be84272338
[b3/fd0587] 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 Sort
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-27a08ce045b53f1bde6e39f497d45d7c.nf` [zen_golick] DSL2 - revision: f69ebed845
[b7/85b2d6] Submitted process > BWA_INDEX (genome.fasta)
WARN: Process `BWA_INDEX` publishDir path contains a variable with a null value
[3e/7ec0ca] 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 - fastq, index, fasta, false
Assertion failed:
1 of 2 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-ed4be5f8101e3149a8f921495eb18bd1.nf` [loquacious_roentgen] DSL2 - revision: 6cf6ebac0b
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:
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-8b9fbda3a86982967a817867f87058c9.nf` [mad_joliot] DSL2 - revision: 95dfc7498d
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:
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-996f7ae2066691a85efc1f62237ee0a0.nf` [naughty_lagrange] DSL2 - revision: 4da7ce5f61
Nextflow stderr:
Check failure on line 1 in Test Process CNVKIT_GENEMETRICS
github-actions / JUnit Test Report
Test Process CNVKIT_GENEMETRICS.test-cnvkit-genemetrics-with-cns
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-d86a1b858dbff119247dc6f16735d51f.nf` [hopeful_linnaeus] DSL2 - revision: d7e0e6314a
Nextflow stderr:
Check failure on line 1 in Test Process CONTROLFREEC_ASSESSSIGNIFICANCE
github-actions / JUnit Test Report
Test Process CONTROLFREEC_ASSESSSIGNIFICANCE.human - freec_ratio - 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-f3a6934daa452cc8cd0beaeaa64eafda.nf` [zen_wiles] DSL2 - revision: 66b9d3a038
[2f/c0308b] 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
[92/e81142] Submitted process > CONTROLFREEC_FREEC (test)
WARN: Process `CONTROLFREEC_FREEC` publishDir path contains a variable with a null value
[6d/65e800] 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 - [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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-55517b61b9cb0cae806dc65e7afc316a.nf` [peaceful_venter] DSL2 - revision: 518d773ebb
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, 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-a127856adaddf53f996e5e276ed73834.nf` [intergalactic_liskov] DSL2 - revision: 6dceb8565a
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 - 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-3d5e3a7421bac756b832552a6703e39e.nf` [stoic_monod] 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 FASTP
github-actions / JUnit Test Report
Test Process FASTP.test_fastp_single_end
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-c58d2d608195f25faaea707573de3998.nf` [adoring_ekeblad] DSL2 - revision: 9c239b6cfe
[1e/016757] 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 FASTP
github-actions / JUnit Test Report
Test Process FASTP.test_fastp_paired_end_merged
Assertion failed:
2 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-e4d55a527e99e7049f3a388d80d0a282.nf` [furious_edison] DSL2 - revision: e957de6de3
[4d/ce6a8b] 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 FGBIO_CALLMOLECULARCONSENSUSREADS
github-actions / JUnit Test Report
Test Process FGBIO_CALLMOLECULARCONSENSUSREADS.homo_sapiens - 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-560c5f92a229a858d3ed8ba8b386726d.nf` [insane_darwin] 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-560c5f92a229a858d3ed8ba8b386726d.nf' at line: 11 or see '/home/runner/work/sarek/sarek/.nf-test/tests/560c5f92a229a858d3ed8ba8b386726d/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 - [ cram, crai, cram, crai, 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-b63773b2e77ac99761d31388d20d5850.nf` [happy_mahavira] DSL2 - revision: a0eec4e010
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` [golden_gautier] DSL2 - revision: 4948fc9022
[6d/70f331] 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` [magical_magritte] DSL2 - revision: b5ad5c616e
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam
[1b/c6e3f0] 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` [high_sanger] DSL2 - revision: 121728c0b1
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_GENOTYPEGVCFS
github-actions / JUnit Test Report
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gendb, [], [], []], 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-ab726c0d2aa337de169fb7541df07e9e.nf` [chaotic_hypatia] DSL2 - revision: d0ac583623
[ea/40a906] Submitted process > UNTAR (test_genomicsdb.tar.gz)
WARN: Process `UNTAR` publishDir path contains a variable with a null value
[06/464d8a] Submitted process > GATK4_GENOTYPEGVCFS (test)
Nextflow stderr:
Check failure on line 1 in Test Process GATK4SPARK_APPLYBQSR
github-actions / JUnit Test Report
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - 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-76a0510efed4985368a5c2abed8da308.nf` [kickass_ride] DSL2 - revision: 0470a34d82
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-76a0510efed4985368a5c2abed8da308.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/76a0510efed4985368a5c2abed8da308/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, [] - window
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-4fb5cdcb3ff20c24a9c710f12ca52ee.nf` [pedantic_pauling] DSL2 - revision: ecf3b8da18
[4d/d7a296] 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
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-14638fb7ac33d32e9c6604b7a046e5a1.nf` [clever_jang] DSL2 - revision: abf84489a3
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 NGSCHECKMATE_NCM
github-actions / JUnit Test Report
Test Process NGSCHECKMATE_NCM.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-9f52122d4e2466a5fc43264e843ee06c.nf` [zen_khorana] DSL2 - revision: 48e42ff83d
ERROR ~ No such file or directory: Can't find a matching module file for include: /home/runner/work/sarek/sarek/modules/nf-core/ngscheckmate/ncm/tests/../../../bedtools/makewindows/main.nf
-- Check script '/home/runner/work/sarek/sarek/.nf-test-9f52122d4e2466a5fc43264e843ee06c.nf' at line: 11 or see '/home/runner/work/sarek/sarek/.nf-test/tests/9f52122d4e2466a5fc43264e843ee06c/meta/nextflow.log' file for more details
Nextflow stderr: