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Revert "Update FastQC and UMItools modules" #2097

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Revert "Update FastQC and UMItools modules"

Revert "Update FastQC and UMItools modules" #2097

Triggered via pull request January 3, 2024 14:18
@pinin4fjordspinin4fjords
opened #1148
revert-1138-dev
Status Failure
Total duration 11m 27s
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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10 errors and 23 warnings
Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
Process completed with exit code 1.
Test STAR Salmon with workflow parameters (--with_umi)
The operation was canceled.
Test STAR Salmon with workflow parameters (--save_align_intermeds --save_reference)
The operation was canceled.
Test STAR Salmon with workflow parameters (--transcript_fasta false)
The operation was canceled.
Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
The operation was canceled.
Test STAR Salmon with workflow parameters (--skip_trimming)
The operation was canceled.
Test STAR Salmon with workflow parameters (--gtf false)
The operation was canceled.
Test STAR Salmon with workflow parameters (--featurecounts_group_type false)
The operation was canceled.
Test STAR Salmon with workflow parameters (--star_index false)
The operation was canceled.
Test STAR Salmon with workflow parameters (--bam_csi_index)
The operation was canceled.
Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --skip_alignment --skip_p...
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 Pseudoaligners with workflow parameters (--pseudo_aligner salmon --skip_alignment --skip_pse...
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 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 Pseudoaligners with workflow parameters (--pseudo_aligner salmon --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 (--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 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)
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 (--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 (--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 (--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 Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
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 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 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 (--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 (--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 (--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 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 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 Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_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/