Merge pull request #1274 from adamrtalbot/update_bam_markduplicates_p… #2481

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Triggered via push April 5, 2024 17:58

adamrtalbot

dev

Status Failure

Total duration 13m 44s

Artifacts –

ci.yml

on: push

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

Matrix: test

Waiting for pending jobs

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3 errors and 17 warnings

confirm-pass

Process completed with exit code 1.

Error when evaluating 'strategy' for job 'test'. .github/workflows/ci.yml (Line: 187, Col: 16): Error parsing fromJson,.github/workflows/ci.yml (Line: 187, Col: 16): Error reading JToken from JsonReader. Path '', line 0, position 0.

Run with profile test: Run with profile test#L1

Assertion failed: 1 of 1 assertions failed

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/.

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 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 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 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 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 (--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 (--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 (--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 (--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 (--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/.