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Move process config into pipeline code #1889

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Move process config into pipeline code

Move process config into pipeline code #1889

Triggered via pull request October 6, 2023 14:44
@bentshermanbentsherman
synchronize #1081
bentsherman:programmatic-process-config
Status Failure
Total duration 1m 10s
Artifacts –

ci.yml

on: pull_request
Matrix: Test HISAT2 with workflow parameters
Matrix: Test Salmon 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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23 errors and 20 warnings
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
Process completed with exit code 1.
Test HISAT2 with workflow parameters (--skip_qc)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--trimmer fastp)
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 (--save_align_intermeds --save_reference)
Process completed with exit code 1.
Test STAR RSEM with workflow parameters (--skip_qc)
Process completed with exit code 1.
Test HISAT2 with workflow parameters (--hisat2_index false)
Process completed with exit code 1.
Test Salmon with workflow parameters (--skip_alignment --skip_pseudo_alignment)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--bam_csi_index)
The operation was canceled.
Test STAR Salmon with workflow parameters (--star_index false)
The operation was canceled.
Run pipeline with test data (22.10.1)
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 (--with_umi)
The operation was canceled.
Test STAR Salmon with workflow parameters (--skip_trimming)
The operation was canceled.
Test Salmon with workflow parameters (--salmon_index false --transcript_fasta false)
The operation was canceled.
Test STAR Salmon with workflow parameters (--gtf false)
The operation was canceled.
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
The operation was canceled.
Test STAR Salmon with workflow parameters (--transcript_fasta false)
The operation was canceled.
Run pipeline with test data (latest-everything)
The job was canceled because "_22_10_1" failed.
Run pipeline with test data (latest-everything)
The operation was canceled.
Test Salmon with workflow parameters (--skip_qc)
The operation was canceled.
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
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 (--featurecounts_group_type 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 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/
Test STAR Salmon with workflow parameters (--min_mapped_reads 90)
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 (--trimmer fastp)
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)
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 (--save_align_intermeds --save_reference)
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 (--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 (--hisat2_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 Salmon with workflow parameters (--skip_alignment --skip_pseudo_alignment)
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 (--bam_csi_index)
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 (--star_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 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 (--with_umi)
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_trimming)
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 Salmon with workflow parameters (--salmon_index false --transcript_fasta 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 (--gtf 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 (--with_umi --skip_trimming)
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 (--transcript_fasta 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 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/