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Subworkflow/bam generation with mskcc modules only #7

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Subworkflow/bam generation with mskcc modules only

Subworkflow/bam generation with mskcc modules only #7

Re-run triggered October 9, 2023 14:44
@anoronh4anoronh4
#4
anoronh4:subworkflow/bam_generation_msk_only
Status Cancelled
Total duration 8m 25s
Artifacts 1

test.yml

on: pull_request
pytest-changes
4s
pytest-changes
prettier
2m 14s
prettier
editorconfig
11s
editorconfig
Matrix: nf-core-lint
Matrix: pytest
confirm-pass
2s
confirm-pass
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Annotations

18 errors and 13 warnings
nf-core-lint (subworkflows/bwa_markdup_bqsr)
Process completed with exit code 1.
pytest (gatk4/baserecalibratorspark, conda)
Process completed with exit code 1.
pytest (gatk4/markduplicatesspark, conda)
Process completed with exit code 1.
pytest (bwa/mem, conda)
Canceling since a higher priority waiting request for 'test-4' exists
pytest (bwa/mem, conda)
The operation was canceled.
pytest (samtools/index, conda)
Canceling since a higher priority waiting request for 'test-4' exists
pytest (samtools/index, conda)
The operation was canceled.
pytest (gatk4/baserecalibratorspark, singularity)
The operation was canceled.
pytest (gatk4/baserecalibrator, singularity)
The operation was canceled.
pytest (gatk4/markduplicatesspark, singularity)
The operation was canceled.
pytest (gatk4/applybqsrspark, singularity)
The operation was canceled.
pytest (subworkflows/bwa_markdup_bqsr, conda)
Canceling since a higher priority waiting request for 'test-4' exists
pytest (subworkflows/bwa_markdup_bqsr, conda)
The operation was canceled.
pytest (subworkflows/bwa_markdup_bqsr, singularity)
The operation was canceled.
pytest (gatk4/baserecalibrator, conda)
Canceling since a higher priority waiting request for 'test-4' exists
pytest (gatk4/baserecalibrator, conda)
The operation was canceled.
pytest (gatk4/markduplicates, singularity)
The operation was canceled.
confirm-pass
Process completed with exit code 1.
pytest (bwa/mem, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/createsequencedictionary, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/applybqsr, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (samtools/faidx, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/baserecalibratorspark, conda)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (samtools/index, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/markduplicatesspark, conda)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/upload-artifact@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/baserecalibratorspark, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/baserecalibrator, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/markduplicatesspark, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/applybqsrspark, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (subworkflows/bwa_markdup_bqsr, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
pytest (gatk4/markduplicates, singularity)
The following actions uses node12 which is deprecated and will be forced to run on node16: eWaterCycle/setup-singularity@v7. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

Artifacts

Produced during runtime
Name Size
logs-conda- Expired
1.76 MB