74 tests run, 41 passed, 0 skipped, 33 failed.
Annotations
Check failure on line 1 in Test Process BCFTOOLS_ANNOTATE
github-actions / JUnit Test Report
Test Process BCFTOOLS_ANNOTATE.sarscov2 - [vcf, [], 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-aa8b62228e7b586f5319cb9f9e3fdcb0.nf` [stupefied_lovelace] DSL2 - revision: 3bbdce4d42
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-aa8b62228e7b586f5319cb9f9e3fdcb0.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/aa8b62228e7b586f5319cb9f9e3fdcb0/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], [] - 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-a8451f450595c5001f45300d6511656.nf` [magical_lichterman] DSL2 - revision: a01a43d4bb
Process `BCFTOOLS_ANNOTATE` declares 4 input channels but 2 were specified
-- Check script '/home/runner/work/sarek/sarek/.nf-test-a8451f450595c5001f45300d6511656.nf' at line: 44 or see '/home/runner/work/sarek/sarek/.nf-test/tests/a8451f450595c5001f45300d6511656/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
Assertion failed:
5 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-a52a407c15c0da01d05be1c739da58e5.nf` [tender_volta] DSL2 - revision: 804fd5d270
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
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-db135e932f528e12d7126a44057e4836.nf` [nauseous_lattes] DSL2 - revision: be84272338
[88/fbb1b4] 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_csi - 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-f97631f4fcfca1846f3ea6ba1fd78820.nf` [high_lamarr] DSL2 - revision: be84272338
[7d/3182de] 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 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-42230dbe123df2f99632f6dbe75ece1b.nf` [drunk_linnaeus] DSL2 - revision: cab0ca230f
[a1/84810c] Submitted process > BWA_INDEX (genome.fasta)
WARN: Process `BWA_INDEX` publishDir path contains a variable with a null value
[cc/46f729] 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, 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-52fa0d2217318220d5a3490f900f5fa4.nf` [cheesy_faraday] DSL2 - revision: c64d48493d
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 hybrid mode - bam
java.lang.NullPointerException: Cannot invoke method getAt() on null object
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-fc438db575bababb4a6f66ac343408c6.nf` [astonishing_leibniz] DSL2 - revision: d080a1761d
Nextflow stderr:
Check failure on line 1 in Test Process CNVKIT_BATCH
github-actions / JUnit Test Report
Test Process CNVKIT_BATCH.cnvkit batch germline 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-3c695a64203190e2ed69ae6bdc34d119.nf` [sick_brown] DSL2 - revision: cd776bec1e
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] - 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-ff87ec3fed425dabc30eb6cc831f4c13.nf` [peaceful_angela] 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 DRAGMAP_ALIGN
github-actions / JUnit Test Report
Test Process DRAGMAP_ALIGN.sarscov2 - fastq, 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-7546220133dde66e0e7726c96703bbdb.nf` [big_nightingale] DSL2 - revision: af0c5fcfc5
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_ALIGN
github-actions / JUnit Test Report
Test Process DRAGMAP_ALIGN.sarscov2 - [fastq1, fastq2], hashtable, fasta, true - 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-33cb4b8e473cc9b6465709f90895f701.nf` [evil_gutenberg] 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_VEP
github-actions / JUnit Test Report
Test Process ENSEMBLVEP_VEP.test_ensemblvep_vep_fasta_vcf
Assertion failed:
2 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-8a3c673bffc0ddff2c4ab4c88a71ee12.nf` [awesome_gautier] DSL2 - revision: 3548fcde48
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 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-9a576f8326ef1386c3e350f64c0c98c5.nf` [focused_panini] DSL2 - revision: 062f412c89
[e3/2fca28] 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_qc_only
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-68e563432bf003338910d8317d706151.nf` [furious_rutherford] DSL2 - revision: d71cbba413
[f2/f52e8f] 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 - [ cram, crai ] - 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-91365d493da151f62409f8391ca7c59f.nf` [ridiculous_pare] DSL2 - revision: 05f6b7027f
Nextflow stderr:
Check failure on line 1 in Test Process GATK4_APPLYBQSR
github-actions / JUnit Test Report
Test Process GATK4_APPLYBQSR.sarscov2 - cram
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-e09b8f6d5dcc6a79c15bbb9fdcc1a2f2.nf` [furious_raman] DSL2 - revision: 675f8b19b6
[25/66345f] 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.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-c26593249022e59a5fc168e31f3cd221.nf` [nice_roentgen] DSL2 - revision: 6513c12b9c
[f3/31f1d7] 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_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 24.09.0-edge
Launching `/home/runner/work/sarek/sarek/.nf-test-777d06bf58c12c4e5bffe73c682ce47d.nf` [furious_angela] DSL2 - revision: 7f70333bc6
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` [astonishing_venter] DSL2 - revision: d0ac583623
[a0/662e15] Submitted process > UNTAR (test_genomicsdb.tar.gz)
WARN: Process `UNTAR` publishDir path contains a variable with a null value
[03/064fdb] 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` [insane_hypatia] 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` [golden_bell] DSL2 - revision: ecf3b8da18
[e5/283d0c] 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` [adoring_curry] 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` [deadly_mercator] 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:
Check failure on line 1 in Test Process SAMBLASTER
github-actions / JUnit Test Report
Test Process SAMBLASTER.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-8a53ca86ecb60fc8c6d8ae819700f12d.nf` [amazing_hodgkin] DSL2 - revision: c315163a44
Staging foreign file: s3://ngi-igenomes/testdata/nf-core/modules/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam
[ce/71f3d9] Submitted process > SAMBLASTER (test)
Nextflow stderr: