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Refactor ext config as process inputs #1

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Refactor ext config as process inputs

Refactor ext config as process inputs #1

Triggered via pull request April 23, 2024 04:03
@bentshermanbentsherman
opened #1
refactor-ext-config
Status Failure
Total duration 2m 40s
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
Matrix: Run pipeline with test data
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39 errors and 9 warnings
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_qc)
Process completed with exit code 1.
Test STAR RSEM with workflow parameters (--rsem_index false)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--skip_qc)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
Process completed with exit code 1.
Test HISAT2 with workflow parameters (--skip_qc)
Process completed with exit code 1.
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
The job was canceled because "_--pseudo_aligner_kallist" failed.
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_qc)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--gtf false)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--gtf false)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--with_umi)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--skip_trimming)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--trimmer fastp)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--star_index false)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
The job was canceled because "_--skip_qc" failed.
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
The job was canceled because "_--pseudo_aligner_kallist" failed.
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--transcript_fasta false)
The job was canceled because "_--skip_qc" failed.
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index false --...
The job was canceled because "_--pseudo_aligner_kallist" failed.
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index false --...
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
Process completed with exit code 1.
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
The job was canceled because "_--pseudo_aligner_kallist" failed.
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
The operation was canceled.
Test STAR RSEM with workflow parameters (--skip_qc)
The job was canceled because "_--rsem_index_false" failed.
Test STAR RSEM with workflow parameters (--skip_qc)
Process completed with exit code 1.
Test HISAT2 with workflow parameters (--hisat2_index false)
The job was canceled because "_--skip_qc" failed.
Test HISAT2 with workflow parameters (--hisat2_index false)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--bam_csi_index)
The job was canceled because "_--skip_qc" failed.
Test STAR Salmon with workflow parameters (--bam_csi_index)
The operation was canceled.
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
The job was canceled because "_--pseudo_aligner_kallist" failed.
Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
The operation was canceled.
Run pipeline with test data (23.04.0)
Process completed with exit code 1.
Run pipeline with test data (latest-everything)
The job was canceled because "_23_04_0" failed.
Run pipeline with test data (latest-everything)
The operation was canceled.
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: actions/checkout@v2. 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)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
Test STAR RSEM with workflow parameters (--rsem_index false)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2. 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 (--rsem_index false)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
Test STAR Salmon with workflow parameters (--skip_qc)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2. 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)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
Test HISAT2 with workflow parameters (--skip_qc)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2. 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)
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
Run pipeline with test data (23.04.0)
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.