added indexcov : finding large INDEL using the BAI index #196
Triggered via pull request
December 10, 2024 11:08
nf-core-bot
Status
Failure
Total duration
20m 27s
Artifacts
–
pytest.yml
on: pull_request
Check for changes (pytest)
4s
Matrix: pytest
confirm-pass
0s
Annotations
5 errors and 25 warnings
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haplotypecaller_skip_filter docker NF 24.04.2
Process returned exit code 1
Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh"
Launched at "/home/runner/work/sarek/sarek"
Attempts exhausted, made 3 attempts :
Attempt #1 started at : 11:12:10 GMT+0000 (Coordinated Universal Time)
Attempt #2 started at : 11:15:10 GMT+0000 (Coordinated Universal Time)
Attempt #3 started at : 11:17:08 GMT+0000 (Coordinated Universal Time)
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haplotypecaller_skip_filter docker NF latest-everything
Process returned exit code 1
Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh"
Launched at "/home/runner/work/sarek/sarek"
Attempts exhausted, made 3 attempts :
Attempt #1 started at : 11:12:28 GMT+0000 (Coordinated Universal Time)
Attempt #2 started at : 11:15:30 GMT+0000 (Coordinated Universal Time)
Attempt #3 started at : 11:17:23 GMT+0000 (Coordinated Universal Time)
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haplotypecaller docker NF latest-everything
Process returned exit code 1
Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh"
Launched at "/home/runner/work/sarek/sarek"
Attempts exhausted, made 3 attempts :
Attempt #1 started at : 11:13:41 GMT+0000 (Coordinated Universal Time)
Attempt #2 started at : 11:18:14 GMT+0000 (Coordinated Universal Time)
Attempt #3 started at : 11:20:32 GMT+0000 (Coordinated Universal Time)
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haplotypecaller docker NF 24.04.2
Process returned exit code 1
Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh"
Launched at "/home/runner/work/sarek/sarek"
Attempts exhausted, made 3 attempts :
Attempt #1 started at : 11:13:34 GMT+0000 (Coordinated Universal Time)
Attempt #2 started at : 11:18:04 GMT+0000 (Coordinated Universal Time)
Attempt #3 started at : 11:20:29 GMT+0000 (Coordinated Universal Time)
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confirm-pass
Process completed with exit code 1.
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Check for changes (pytest)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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msisensorpro docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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msisensorpro docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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deepvariant docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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deepvariant docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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concatenate_vcfs docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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mpileup docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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concatenate_vcfs docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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haplotypecaller_skip_filter docker NF 24.04.2
No files were found with the provided path: /home/ubuntu/pytest_workflow_*/*/.nextflow.log
/home/ubuntu/pytest_workflow_*/*/log.out
/home/ubuntu/pytest_workflow_*/*/log.err
/home/ubuntu/pytest_workflow_*/*/work
!/home/ubuntu/pytest_workflow_*/*/work/conda
!/home/ubuntu/pytest_workflow_*/*/work/singularity
!/home/runner/work/sarek/sarek/.singularity. No artifacts will be uploaded.
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haplotypecaller_skip_filter docker NF latest-everything
No files were found with the provided path: /home/ubuntu/pytest_workflow_*/*/.nextflow.log
/home/ubuntu/pytest_workflow_*/*/log.out
/home/ubuntu/pytest_workflow_*/*/log.err
/home/ubuntu/pytest_workflow_*/*/work
!/home/ubuntu/pytest_workflow_*/*/work/conda
!/home/ubuntu/pytest_workflow_*/*/work/singularity
!/home/runner/work/sarek/sarek/.singularity. No artifacts will be uploaded.
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joint_germline docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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manta docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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manta docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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mpileup docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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tiddit docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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tiddit docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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cnvkit docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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haplotypecaller docker NF latest-everything
No files were found with the provided path: /home/ubuntu/pytest_workflow_*/*/.nextflow.log
/home/ubuntu/pytest_workflow_*/*/log.out
/home/ubuntu/pytest_workflow_*/*/log.err
/home/ubuntu/pytest_workflow_*/*/work
!/home/ubuntu/pytest_workflow_*/*/work/conda
!/home/ubuntu/pytest_workflow_*/*/work/singularity
!/home/runner/work/sarek/sarek/.singularity. No artifacts will be uploaded.
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cnvkit docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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haplotypecaller docker NF 24.04.2
No files were found with the provided path: /home/ubuntu/pytest_workflow_*/*/.nextflow.log
/home/ubuntu/pytest_workflow_*/*/log.out
/home/ubuntu/pytest_workflow_*/*/log.err
/home/ubuntu/pytest_workflow_*/*/work
!/home/ubuntu/pytest_workflow_*/*/work/conda
!/home/ubuntu/pytest_workflow_*/*/work/singularity
!/home/runner/work/sarek/sarek/.singularity. No artifacts will be uploaded.
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freebayes docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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mutect2 docker NF 24.04.2
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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mutect2 docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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freebayes docker NF latest-everything
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
confirm-pass
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
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