Add nf-test sharding CI #22
73 tests run, 38 passed, 0 skipped, 35 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-5205203429b04daa213d34d362219af3.nf` [grave_fourier] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-f8ea7c8fb29eedc9a9c837e0ed3ee91a.nf` [gigantic_chandrasekhar] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-8ac76e42363269bbc2f145695ad2fae4.nf` [marvelous_church] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-1a5f0352cead0d009265ad64db0f029e.nf` [goofy_angela] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-44e4658d575ca4d2b322c5468e5b2101.nf` [silly_allen] DSL2 - revision: be84272338
[2a/2e8abf] 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 - no 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-ae8f3f6e323f3a92659053719fda7b38.nf` [astonishing_perlman] DSL2 - revision: cb8f8c2ca8
[89/cca373] Submitted process > BWA_INDEX (genome.fasta)
WARN: Process `BWA_INDEX` publishDir path contains a variable with a null value
[4f/1ba0dd] 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, 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-bcc5375c772b31c142ac8958729bac4d.nf` [reverent_leibniz] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-98b23e12ef50d69147dc338977202830.nf` [lethal_shaw] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-5f896e0cc48445bb4d69274fea79eafd.nf` [cheeky_ritchie] DSL2 - revision: fc4f01d0a9
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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-c0b389dfc4bbaa4247bfcc8937e4176e.nf` [nauseous_pare] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-20a793b30e049bd7d222138b2a04fecf.nf` [cranky_joliot] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-8048e98d0283bd73f99a7c91b716e256.nf` [tiny_kay] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-6e218af819229bc0e002268668aaea8f.nf` [lonely_wing] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-14ead4ea0d7ecbb2734396b10c682029.nf` [cranky_mandelbrot] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-8711bc8a4f139041763bf1c226715a23.nf` [nasty_leakey] DSL2 - revision: 9cddfe4326
[9d/a90a90] 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_adapterlist
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-a5cdf7a2217ae0d6290ef653bc07b9cc.nf` [loquacious_aryabhata] DSL2 - revision: 120969a847
[d0/642985] 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 - stub
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-47cedca04cdabf8e73f1dc4f550ecc83.nf` [pedantic_neumann] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-c1f0c01cc4505636ab01fbf576bcb828.nf` [prickly_hodgkin] 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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-87d2475a2777b4a95aa00a67dc3f7e21.nf` [drunk_stonebraker] DSL2 - revision: e17171bd45
[29/04b97d] 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 - multiple sites
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-416b04d7bd8f043e10869fbccf1ceb6d.nf` [chaotic_aryabhata] DSL2 - revision: 39b715024b
[64/eaa386] 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.homo_sapiens - 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-b7f3bb99b7cc55b0ea32e54f131c8e5c.nf` [exotic_jang] DSL2 - revision: 92ef6ec0a5
[f6/4924a1] 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_GENOTYPEGVCFS
github-actions / JUnit Test Report
Test Process GATK4_GENOTYPEGVCFS.homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_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-ec14820ffaaed79e89bdd8e06dce953b.nf` [high_kay] DSL2 - revision: 4ba423f236
[fa/c6e568] Submitted process > UNTAR (test_genomicsdb.tar.gz)
[3e/4ede33] 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] - 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-1369ef3c6626c54340f532598d7f7596.nf` [distracted_ramanujan] DSL2 - revision: d30bb998e3
Nextflow stderr:
Check failure on line 1 in Test Process GATK4SPARK_APPLYBQSR
github-actions / JUnit Test Report
Test Process GATK4SPARK_APPLYBQSR.sarscov2 - bam intervals
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-19afb6f8c6e46fbb3132ef7bc4dc5f0f.nf` [desperate_kimura] DSL2 - revision: b667266299
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-19afb6f8c6e46fbb3132ef7bc4dc5f0f.nf' at line: 34 or see '/home/runner/work/sarek/sarek/.nf-test/tests/19afb6f8c6e46fbb3132ef7bc4dc5f0f/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 - metrics
Assertion failed:
6 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-fc00cd5fb5ccdd893be5e51d42baa177.nf` [insane_laplace] 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-fc00cd5fb5ccdd893be5e51d42baa177.nf' at line: 35 or see '/home/runner/work/sarek/sarek/.nf-test/tests/fc00cd5fb5ccdd893be5e51d42baa177/meta/nextflow.log' file for more details
Nextflow stderr: