Merge pull request #1221 from adamrtalbot/nf-test-cicd #2289
maxulysseci.yml
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Check for changes
6s
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: test
confirm-pass
0s
Annotations
14 errors and 82 warnings
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Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index false --...
Process completed with exit code 1.
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Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
The job was canceled because "_--pseudo_aligner_kalli_3" failed.
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Test Pseudoaligners with workflow parameters (--pseudo_aligner salmon --salmon_index false --tran...
The operation was canceled.
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Test STAR Salmon with workflow parameters (--with_umi --skip_trimming)
Process completed with exit code 1.
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Test STAR Salmon with workflow parameters (--trimmer fastp)
The job was canceled because "_--with_umi_--skip_trimmi" failed.
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Test STAR Salmon with workflow parameters (--trimmer fastp)
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Test STAR Salmon with workflow parameters (--with_umi)
The job was canceled because "_--with_umi_--skip_trimmi" failed.
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Test STAR Salmon with workflow parameters (--with_umi)
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Test STAR Salmon with workflow parameters (--transcript_fasta false)
The job was canceled because "_--with_umi_--skip_trimmi" failed.
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Test STAR Salmon with workflow parameters (--transcript_fasta false)
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Test STAR Salmon with workflow parameters (--star_index false)
The job was canceled because "_--with_umi_--skip_trimmi" failed.
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Test STAR Salmon with workflow parameters (--star_index false)
The operation was canceled.
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Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
The job was canceled because "_--with_umi_--skip_trimmi" failed.
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Test STAR Salmon with workflow parameters (--remove_ribo_rna --skip_qualimap)
The operation was canceled.
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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/.
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BAM_SORT_STATS_SAMTOOLS 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/.
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BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS 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/.
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BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG 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/.
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BBMAP_BBSPLIT 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/.
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BAM_RSEQC 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/.
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CUSTOM_CATADDITIONALFASTA 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/.
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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/.
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CUSTOM_GETCHROMSIZES 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/.
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CUSTOM_TX2GENE 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/.
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GUNZIP 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/.
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HISAT2_EXTRACTSPLICESITES 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/.
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FASTQ_SUBSAMPLE_FQ_SALMON 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/.
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FASTQ_ALIGN_HISAT2 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/.
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HISAT2_BUILD 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/.
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GFFREAD 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/.
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KALLISTO_INDEX 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/.
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FASTQ_FASTQC_UMITOOLS_FASTP 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/.
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FQ_SUBSAMPLE 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/.
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CAT_FASTQ 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/.
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KALLISTO_QUANT 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/.
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RSEQC_BAMSTAT 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/.
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RSEQC_INFEREXPERIMENT 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/.
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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/.
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RSEM_PREPAREREFERENCE 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/.
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PRESEQ_LCEXTRAP 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/.
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RSEQC_READDUPLICATION 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/.
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RSEQC_INNERDISTANCE 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/.
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QUALIMAP_RNASEQ 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/.
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SAMTOOLS_FLAGSTAT 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/.
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SAMTOOLS_IDXSTATS 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/.
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RSEQC_JUNCTIONANNOTATION 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/.
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RSEQC_READDISTRIBUTION 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/.
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RSEQC_JUNCTIONSATURATION 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/.
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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/.
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FASTQ_FASTQC_UMITOOLS_TRIMGALORE 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/.
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RSEQC_TIN 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/.
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HISAT2_ALIGN 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/.
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SALMON_INDEX 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/.
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MULTIQC 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/.
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BAM_STATS_SAMTOOLS 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/.
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SAMTOOLS_INDEX 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/.
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SAMTOOLS_SORT 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/.
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SUBREAD_FEATURECOUNTS 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/.
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UCSC_BEDGRAPHTOBIGWIG 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/.
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STAR_GENOMEGENERATE 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/.
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SAMTOOLS_STATS 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/.
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UCSC_BEDCLIP 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/.
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FASTP 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/.
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STRINGTIE_STRINGTIE 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/.
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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/.
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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/.
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SALMON_QUANT 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/.
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UTILS_NFVALIDATION_PLUGIN 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/.
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RSEM_CALCULATEEXPRESSION 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/.
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UTILS_NEXTFLOW_PIPELINE 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/.
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UMITOOLS_DEDUP 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/.
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UTILS_NFCORE_PIPELINE 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/.
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SORTMERNA 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/.
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TXIMETA_TXIMPORT 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/.
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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/.
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UMITOOLS_PREPAREFORRSEM 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/.
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TRIMGALORE 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/.
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UMITOOLS_EXTRACT 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/.
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Test HISAT2 with workflow parameters (--hisat2_index 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/.
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FASTQC 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/.
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SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT 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/.
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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/.
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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: nf-core/[email protected]. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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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/.
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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/.
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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/.
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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/.
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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/.
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Test STAR Salmon with workflow parameters (--gtf 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/.
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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/.
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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/.
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UNTAR 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/.
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Test Pseudoaligners with workflow parameters (--pseudo_aligner kallisto --kallisto_index 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/.
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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/.
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STAR_ALIGN 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/.
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PIPELINE 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/.
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