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Don't convert input bam files that are supplied in post-alignment steps, it's not necessary. #114

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Don't convert input bam files that are supplied in post-alignment steps, it's not necessary.

Don't convert input bam files that are supplied in post-alignment steps, it's not necessary. #114

Triggered via pull request November 8, 2024 17:26
@FriederikeHanssenFriederikeHanssen
synchronize #1728
FriederikeHanssen:noconversion
Status Failure
Total duration 13m 15s
Artifacts –

pytest.yml

on: pull_request
Check for changes (pytest)
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Matrix: pytest
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13 errors and 6 warnings
recalibrate docker NF 24.04.2
Process returned exit code 5 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 : 17:29:31 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 17:29:32 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 17:29:33 GMT+0000 (Coordinated Universal Time)
recalibrate docker NF 24.04.2
Process completed with exit code 1.
gatk4/markduplicates docker NF 24.04.2
Process returned exit code 5 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 : 17:29:33 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 17:29:34 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 17:29:35 GMT+0000 (Coordinated Universal Time)
gatk4/markduplicates docker NF 24.04.2
Process completed with exit code 1.
gatk4/markduplicates docker NF latest-everything
Process returned exit code 5 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 : 17:29:45 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 17:29:46 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 17:29:47 GMT+0000 (Coordinated Universal Time)
gatk4/markduplicates docker NF latest-everything
Process completed with exit code 1.
prepare_recalibration docker NF latest-everything
Process returned exit code 5 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 : 17:29:45 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 17:29:47 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 17:29:47 GMT+0000 (Coordinated Universal Time)
prepare_recalibration docker NF latest-everything
Process completed with exit code 1.
recalibrate docker NF latest-everything
Process returned exit code 5 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 : 17:29:54 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 17:29:55 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 17:29:56 GMT+0000 (Coordinated Universal Time)
recalibrate docker NF latest-everything
Process completed with exit code 1.
prepare_recalibration docker NF 24.04.2
Process returned exit code 5 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 : 17:39:09 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 17:39:11 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 17:39:12 GMT+0000 (Coordinated Universal Time)
prepare_recalibration docker NF 24.04.2
Process completed with exit code 1.
confirm-pass
Process completed with exit code 1.
recalibrate 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.
gatk4/markduplicates 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.
gatk4/markduplicates 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.
prepare_recalibration 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.
recalibrate 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.
prepare_recalibration 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.