Add exists to Schema #860
GitHub Actions / JUnit Test Report
failed
Aug 28, 2023 in 0s
4 tests run, 0 passed, 0 skipped, 4 failed.
Annotations
Check failure on line 1 in Bismark Hisat Single-End
github-actions / JUnit Test Report
Bismark Hisat Single-End
java.nio.file.NoSuchFileException: /home/runner/work/methylseq/methylseq/.nf-test/tests/516571ef1a0ace9548076c68c097da45/output/bismark_hisat/reference_genome/BismarkIndex
Raw output
Nextflow stdout:
WARN: The following invalid input values have been detected:
* --baseDir: /home/runner/work/methylseq/methylseq
* --base-dir: /home/runner/work/methylseq/methylseq
* --outputDir: /home/runner/work/methylseq/methylseq/.nf-test/tests/516571ef1a0ace9548076c68c097da45/output
* --output-dir: /home/runner/work/methylseq/methylseq/.nf-test/tests/516571ef1a0ace9548076c68c097da45/output
ERROR ~ ERROR: Validation of pipeline parameters failed!
-- Check '/home/runner/work/methylseq/methylseq/.nf-test/tests/516571ef1a0ace9548076c68c097da45/meta/nextflow.log' file for details
Nextflow stderr:
[0;31mThe following invalid input values have been detected:
* --fasta_index: string [https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai] does not match pattern ^\S+\.fn?a(sta)?(\.gz)?$ (https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai)
[0m
Check failure on line 1 in Bismark Hisat Single-End With Index
github-actions / JUnit Test Report
Bismark Hisat Single-End With Index
Assertion failed:
assert workflow.success
| |
workflow falseRaw output
Nextflow stdout:
WARN: The following invalid input values have been detected:
* --baseDir: /home/runner/work/methylseq/methylseq
* --base-dir: /home/runner/work/methylseq/methylseq
* --outputDir: /home/runner/work/methylseq/methylseq/.nf-test/tests/9c0497eebb4d1563170da2e9b9bcfd1e/output
* --output-dir: /home/runner/work/methylseq/methylseq/.nf-test/tests/9c0497eebb4d1563170da2e9b9bcfd1e/output
ERROR ~ ERROR: Validation of pipeline parameters failed!
-- Check '/home/runner/work/methylseq/methylseq/.nf-test/tests/9c0497eebb4d1563170da2e9b9bcfd1e/meta/nextflow.log' file for details
Nextflow stderr:
[0;31mThe following invalid input values have been detected:
* --bismark_index: the file or directory '.nf-test/indexes/BismarkIndex/' does not exist.
* --fasta_index: string [https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai] does not match pattern ^\S+\.fn?a(sta)?(\.gz)?$ (https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai)
[0m
Check failure on line 1 in Bismark Hisat Single-End With RRBS
github-actions / JUnit Test Report
Bismark Hisat Single-End With RRBS
Assertion failed:
13 of 13 assertions failed
Raw output
Nextflow stdout:
WARN: The following invalid input values have been detected:
* --baseDir: /home/runner/work/methylseq/methylseq
* --base-dir: /home/runner/work/methylseq/methylseq
* --outputDir: /home/runner/work/methylseq/methylseq/.nf-test/tests/b0548a650999fa17c74f5d9894a9d895/output
* --output-dir: /home/runner/work/methylseq/methylseq/.nf-test/tests/b0548a650999fa17c74f5d9894a9d895/output
ERROR ~ ERROR: Validation of pipeline parameters failed!
-- Check '/home/runner/work/methylseq/methylseq/.nf-test/tests/b0548a650999fa17c74f5d9894a9d895/meta/nextflow.log' file for details
Nextflow stderr:
[0;31mThe following invalid input values have been detected:
* --fasta_index: string [https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai] does not match pattern ^\S+\.fn?a(sta)?(\.gz)?$ (https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai)
[0m
Check failure on line 1 in Bismark Hisat Single-End With RRBS With Index
github-actions / JUnit Test Report
Bismark Hisat Single-End With RRBS With Index
Assertion failed:
assert workflow.success
| |
workflow falseRaw output
Nextflow stdout:
WARN: The following invalid input values have been detected:
* --baseDir: /home/runner/work/methylseq/methylseq
* --base-dir: /home/runner/work/methylseq/methylseq
* --outputDir: /home/runner/work/methylseq/methylseq/.nf-test/tests/878f7d3ae067e2d57ede01e9aedc9daa/output
* --output-dir: /home/runner/work/methylseq/methylseq/.nf-test/tests/878f7d3ae067e2d57ede01e9aedc9daa/output
ERROR ~ ERROR: Validation of pipeline parameters failed!
-- Check '/home/runner/work/methylseq/methylseq/.nf-test/tests/878f7d3ae067e2d57ede01e9aedc9daa/meta/nextflow.log' file for details
Nextflow stderr:
[0;31mThe following invalid input values have been detected:
* --bismark_index: the file or directory '.nf-test/indexes/BismarkIndex/' does not exist.
* --fasta_index: string [https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai] does not match pattern ^\S+\.fn?a(sta)?(\.gz)?$ (https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/reference/genome.fa.fai)
[0m
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