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Update bam_markduplicates_picard subworkflow #2470

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Update bam_markduplicates_picard subworkflow

Update bam_markduplicates_picard subworkflow #2470

Triggered via pull request March 22, 2024 11:42
@adamrtalbotadamrtalbot
synchronize #1274
adamrtalbot:update_bam_markduplicates_picard
Status Success
Total duration 15m 56s
Artifacts –

ci.yml

on: pull_request
Matrix: Test HISAT2 with workflow parameters
Matrix: Test Pseudoaligners with workflow parameters
Matrix: Test STAR RSEM with workflow parameters
Matrix: Test STAR Salmon with workflow parameters
Check for changes
6s
Check for changes
Matrix: test
confirm-pass
0s
confirm-pass
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2 errors and 21 warnings
BAM_MARKDUPLICATES_PICARD docker NF-23.04.0
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
PICARD_MARKDUPLICATES docker NF-23.04.0
❌ Failed to create checks using the provided token. (HttpError: Resource not accessible by integration)
Check for changes
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
BAM_MARKDUPLICATES_PICARD docker NF-23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected], actions/setup-python@v4, actions/cache@v3, mikepenz/action-junit-report@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
BAM_MARKDUPLICATES_PICARD docker NF-23.04.0
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
PICARD_MARKDUPLICATES docker NF-23.04.0
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected], actions/setup-python@v4, actions/cache@v3, mikepenz/action-junit-report@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
PICARD_MARKDUPLICATES docker NF-23.04.0
⚠️ This usually indicates insufficient permissions. More details: https://github.com/mikepenz/action-junit-report/issues/23
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test HISAT2 with workflow parameters (--skip_qc)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR RSEM with workflow parameters (--skip_qc)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--skip_qc)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--bam_csi_index)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--trimmer fastp)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--skip_trimming)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--with_umi)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.