System.IO.IOException: No space left on device : '/home/runner/runners/2.313.0/_diag/Worker_20240215-163025-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id) at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message) at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message) at GitHub.Runner.Worker.Worker.RunAsync(String pipeIn, String pipeOut) at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args) System.IO.IOException: No space left on device : '/home/runner/runners/2.313.0/_diag/Worker_20240215-163025-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/runners/2.313.0/_diag/Worker_20240215-163025-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id) at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message) at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message) at GitHub.Runner.Common.Tracing.Error(Exception exception) at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args) at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at System.Diagnostics.TraceSource.Flush() at GitHub.Runner.Common.TraceManager.Dispose(Boolean disposing) at GitHub.Runner.Common.TraceManager.Dispose() at GitHub.Runner.Common.HostContext.Dispose(Boolean disposing) at GitHub.Runner.Common.HostContext.Dispose() at GitHub.Runner.Worker.Program.Main(String[] args)

nf-test (antismash/antismashlitedownloaddatabases, singularity)

System.IO.IOException: No space left on device : '/home/runner/runners/2.313.0/_diag/Worker_20240215-163025-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id) at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message) at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message) at GitHub.Runner.Worker.Worker.RunAsync(String pipeIn, String pipeOut) at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args) System.IO.IOException: No space left on device : '/home/runner/runners/2.313.0/_diag/Worker_20240215-163025-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at GitHub.Runner.Common.HostTraceListener.WriteHeader(String source, TraceEventType eventType, Int32 id) at GitHub.Runner.Common.HostTraceListener.TraceEvent(TraceEventCache eventCache, String source, TraceEventType eventType, Int32 id, String message) at System.Diagnostics.TraceSource.TraceEvent(TraceEventType eventType, Int32 id, String message) at GitHub.Runner.Common.Tracing.Error(Exception exception) at GitHub.Runner.Worker.Program.MainAsync(IHostContext context, String[] args) Unhandled exception. System.IO.IOException: No space left on device : '/home/runner/runners/2.313.0/_diag/Worker_20240215-163025-utc.log' at System.IO.RandomAccess.WriteAtOffset(SafeFileHandle handle, ReadOnlySpan`1 buffer, Int64 fileOffset) at System.IO.Strategies.BufferedFileStreamStrategy.FlushWrite() at System.IO.StreamWriter.Flush(Boolean flushStream, Boolean flushEncoder) at System.Diagnostics.TextWriterTraceListener.Flush() at System.Diagnostics.TraceSource.Flush() at GitHub.Runner.Common.TraceManager.Dispose(Boolean disposing) at GitHub.Runner.Common.TraceManager.Dispose() at GitHub.Runner.Common.HostContext.Dispose(Boolean disposing) at GitHub.Runner.Common.HostContext.Dispose() at GitHub.Runner.Worker.Program.Main(String[] args)

nf-test (antismash/antismashlitedownloaddatabases, docker)

No space left on device : '/home/runner/runners/2.313.0/_diag/pages/1eaed079-b77d-4c40-a049-fa0ab3f665f1_71ce60d8-a12d-5f36-7800-7664d025c456_1.log'

confirm-pass

Process completed with exit code 1.

nf-test-changes

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: mirpedrol/paths-filter@main. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest-changes

pre-commit

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v3, actions/cache@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

nf-test (bclconvert, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, nf-core/setup-nextflow@v1, actions/cache@v3, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

nf-test (bcftools/view, docker)

nf-test (centrifuge/build, docker)

nf-test (centrifuge/build, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-java@v3, nf-core/setup-nextflow@v1, actions/cache@v3, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

nf-test (custom/dumpsoftwareversions, docker)

nf-test (gatk4/reblockgvcf, docker)

nf-test (famsa/align, docker)

nf-test (gatk4/selectvariants, docker)

nf-test (famsa/align, singularity)

nf-test (bcftools/view, conda)

nf-test (gatk4/mergevcfs, docker)

nf-test (gatk4/splitncigarreads, docker)

nf-test (gatk4/svcluster, docker)

nf-test (custom/dumpsoftwareversions, singularity)

nf-test (bclconvert, singularity)

nf-test (centrifuge/build, conda)

nf-test (gatk4/svannotate, docker)

nf-test (eklipse, docker)

nf-test (famsa/align, conda)

nf-test (clustalo/align, docker)

nf-test (clustalo/align, singularity)

nf-test (gatk4/selectvariants, conda)

nf-test (eklipse, singularity)

nf-test (gatk4/svcluster, conda)

nf-test (eklipse, conda)

nf-test (gatk4/splitncigarreads, singularity)

nf-test (gatk4/svannotate, singularity)

nf-test (gatk4/mergevcfs, conda)

nf-test (gatk4/splitncigarreads, conda)

nf-test (gatk4/mergevcfs, singularity)

nf-test (clustalo/align, conda)

nf-test (gatk4/reblockgvcf, conda)

nf-test (bcftools/view, singularity)

nf-test (gatk4/svcluster, singularity)

nf-test (gatk4/svannotate, conda)

nf-test (gatk4/selectvariants, singularity)

nf-test (hamronization/abricate, docker)

nf-test (hamronization/amrfinderplus, docker)

nf-test (hamronization/amrfinderplus, singularity)

nf-test (gatk4spark/applybqsr, docker)

nf-test (gatk4/reblockgvcf, singularity)

nf-test (hamronization/deeparg, docker)

nf-test (hamronization/amrfinderplus, conda)

nf-test (hamronization/fargene, singularity)

nf-test (hamronization/abricate, conda)

nf-test (hamronization/summarize, docker)

nf-test (hamronization/abricate, singularity)

nf-test (gatk4spark/markduplicates, docker)

nf-test (hamronization/fargene, docker)

nf-test (hamronization/summarize, singularity)

nf-test (mtmalign/align, singularity)

nf-test (mtmalign/align, docker)

nf-test (gatk4spark/applybqsr, conda)

nf-test (hamronization/deeparg, singularity)

nf-test (muscle5/super5, singularity)

nf-test (hamronization/summarize, conda)

nf-test (muscle5/super5, conda)

nf-test (hamronization/fargene, conda)

nf-test (muscle5/super5, docker)

nf-test (deeparg/predict, singularity)

nf-test (multiqc, docker)

nf-test (gatk4spark/markduplicates, singularity)

nf-test (hamronization/deeparg, conda)

nf-test (mtmalign/align, conda)

nf-test (mafft, docker)

nf-test (hamronization/rgi, docker)

nf-test (deeparg/predict, docker)

nf-test (hamronization/rgi, singularity)

nf-test (gatk4spark/markduplicates, conda)

nf-test (mafft, singularity)

nf-test (multiqc, singularity)

nf-test (pyrodigal, docker)

nf-test (pyrodigal, conda)

nf-test (pyrodigal, singularity)

nf-test (rhocall/viz, docker)

nf-test (rhocall/viz, singularity)

nf-test (propr/propr, docker)

nf-test (propr/propr, singularity)

nf-test (deeparg/downloaddata, docker)

nf-test (rhocall/viz, conda)

nf-test (mafft, conda)

nf-test (hamronization/rgi, conda)

nf-test (multiqc, conda)

nf-test (gatk4spark/applybqsr, singularity)

nf-test (deeparg/predict, conda)

nf-test (deeparg/downloaddata, singularity)

nf-test (custom/tx2gene, singularity)

nf-test (rseqc/bamstat, docker)

nf-test (rseqc/readdistribution, singularity)

nf-test (rsem/calculateexpression, docker)

nf-test (gatk4/genomicsdbimport, docker)

nf-test (quartonotebook, docker)

nf-test (rseqc/tin, singularity)

nf-test (custom/tx2gene, docker)

nf-test (samtools/ampliconclip, singularity)

nf-test (samtools/ampliconclip, docker)

nf-test (rseqc/tin, docker)

nf-test (rseqc/readdistribution, docker)

nf-test (samtools/bam2fq, singularity)

nf-test (samtools/bam2fq, docker)

nf-test (samtools/ampliconclip, conda)

nf-test (propr/propr, conda)

nf-test (samtools/calmd, singularity)

nf-test (samtools/bam2fq, conda)

nf-test (salmon/quant, docker)

nf-test (samtools/calmd, docker)

nf-test (rsem/preparereference, docker)

nf-test (salmon/quant, singularity)

nf-test (salmon/index, docker)

nf-test (samtools/cat, docker)

nf-test (samtools/calmd, conda)

nf-test (samtools/cat, conda)

nf-test (samtools/cat, singularity)

nf-test (rsem/calculateexpression, conda)

nf-test (samtools/collate, docker)

nf-test (rsem/preparereference, singularity)

nf-test (samtools/collate, conda)

nf-test (salmon/index, singularity)

nf-test (samtools/collate, singularity)

nf-test (deeparg/downloaddata, conda)

nf-test (quartonotebook, singularity)

nf-test (samtools/fastq, singularity)

nf-test (samtools/convert, conda)

nf-test (samtools/convert, docker)

nf-test (samtools/fastq, conda)

nf-test (rsem/preparereference, conda)

nf-test (samtools/fixmate, conda)

nf-test (samtools/fastq, docker)

nf-test (samtools/convert, singularity)

nf-test (samtools/fixmate, singularity)

nf-test (samtools/fixmate, docker)

nf-test (gatk4/genomicsdbimport, conda)

nf-test (rseqc/bamstat, conda)

nf-test (samtools/mpileup, docker)

nf-test (rseqc/readdistribution, conda)

nf-test (rseqc/tin, conda)

nf-test (samtools/mpileup, singularity)

nf-test (salmon/quant, conda)

nf-test (salmon/index, conda)

nf-test (samtools/mpileup, conda)

nf-test (seqkit/concat, docker)

nf-test (samtools/sort, docker)

nf-test (samtools/sort, singularity)

nf-test (seqkit/concat, singularity)

nf-test (seqkit/concat, conda)

nf-test (samtools/merge, docker)

nf-test (samtools/view, singularity)

nf-test (samtools/idxstats, singularity)

nf-test (samtools/view, docker)

nf-test (stringtie/merge, docker)

nf-test (samtools/flagstat, docker)

nf-test (stringtie/merge, singularity)

nf-test (samtools/idxstats, docker)

nf-test (rsem/calculateexpression, singularity)

nf-test (sortmerna, docker)

nf-test (samtools/merge, conda)

nf-test (stringtie/merge, conda)

nf-test (samtools/flagstat, singularity)

nf-test (subread/featurecounts, conda)

nf-test (subread/featurecounts, docker)

nf-test (stringtie/stringtie, docker)

nf-test (samtools/view, conda)

nf-test (stringtie/stringtie, singularity)

nf-test (subread/featurecounts, singularity)

nf-test (gatk4/genomicsdbimport, singularity)

nf-test (samtools/sort, conda)

nf-test (samtools/index, docker)

nf-test (sortmerna, singularity)

nf-test (subworkflows/bam_dedup_stats_samtools_umitools, docker)

nf-test (subworkflows/bam_markduplicates_picard, docker)

nf-test (subworkflows/bam_rseqc, singularity)

nf-test (subworkflows/bam_sort_stats_samtools, singularity)

nf-test (subworkflows/bam_sort_stats_samtools, docker)

nf-test (samtools/stats, docker)

nf-test (stringtie/stringtie, conda)

nf-test (subworkflows/bam_markduplicates_picard, singularity)

nf-test (subworkflows/bam_dedup_stats_samtools_umitools, singularity)

nf-test (subworkflows/bam_rseqc, docker)

nf-test (subworkflows/bam_dedup_stats_samtools_umitools, conda)

nf-test (subworkflows/utils_nfcore_pipeline, docker)

nf-test (subworkflows/preprocess_rnaseq, docker)

nf-test (samtools/index, singularity)

nf-test (subworkflows/utils_nfcore_pipeline, singularity)

nf-test (svdb/merge, docker)

nf-test (subworkflows/utils_nfcore_pipeline, conda)

nf-test (sortmerna, conda)

nf-test (subworkflows/preprocess_rnaseq, singularity)

nf-test (subworkflows/bam_stats_samtools, singularity)

nf-test (rseqc/bamstat, singularity)

nf-test (svdb/merge, singularity)

nf-test (subworkflows/bam_stats_samtools, docker)

nf-test (subworkflows/fastq_fastqc_umitools_trimgalore, singularity)

nf-test (samtools/stats, singularity)

nf-test (subworkflows/bam_sort_stats_samtools, conda)

nf-test (subworkflows/bam_markduplicates_picard, conda)

nf-test (subworkflows/fastq_fastqc_umitools_trimgalore, docker)

nf-test (svdb/merge, conda)

nf-test (tcoffee/align, docker)

nf-test (tcoffee/align, singularity)

nf-test (subworkflows/bam_rseqc, conda)

nf-test (custom/tx2gene, conda)

nf-test (tcoffee/alncompare, docker)

nf-test (summarizedexperiment/summarizedexperiment, singularity)

nf-core-lint (antismash/antismashlite)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/cache@v3, actions/setup-java@v3, nf-core/setup-nextflow@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

nf-core-lint (antismash/antismashlitedownloaddatabases)

nf-test (summarizedexperiment/summarizedexperiment, docker)

nf-test (tcoffee/irmsd, docker)

nf-test (tcoffee/irmsd, singularity)

nf-test (tcoffee/alncompare, singularity)

nf-test (subworkflows/preprocess_rnaseq, conda)

nf-core-lint (bcftools/view)

nf-test (tcoffee/alncompare, conda)

nf-test (ucsc/bedclip, docker)

nf-core-lint (bclconvert)

nf-test (ucsc/bedgraphtobigwig, docker)

nf-test (trimgalore, docker)

nf-test (samtools/idxstats, conda)

nf-test (ucsc/bedclip, singularity)

nf-test (wfmash, singularity)

nf-core-lint (clustalo/align)

nf-test (samtools/flagstat, conda)

nf-test (wfmash, docker)

nf-test (ucsc/bedclip, conda)

nf-core-lint (custom/tx2gene)

nf-core-lint (deeparg/downloaddata)

nf-core-lint (custom/dumpsoftwareversions)

nf-core-lint (centrifuge/build)

nf-test (wfmash, conda)

nf-core-lint (deeparg/predict)

nf-core-lint (famsa/align)

nf-core-lint (eklipse)

nf-test (umitools/prepareforrsem, docker)

nf-core-lint (gatk4/genomicsdbimport)

nf-core-lint (gatk4/mergevcfs)

nf-test (umitools/prepareforrsem, singularity)

nf-test (ucsc/bedgraphtobigwig, singularity)

nf-test (umitools/prepareforrsem, conda)

nf-core-lint (gatk4/selectvariants)

nf-test (ucsc/bedgraphtobigwig, conda)

nf-core-lint (gatk4/splitncigarreads)

nf-core-lint (gatk4/reblockgvcf)

nf-core-lint (gatk4spark/applybqsr)

nf-core-lint (gsea/gsea)

nf-test (tcoffee/irmsd, conda)

nf-core-lint (gatk4/svannotate)

nf-core-lint (hamronization/amrfinderplus)

nf-core-lint (gatk4/svcluster)

nf-core-lint (hamronization/rgi)

nf-core-lint (hamronization/fargene)

nf-core-lint (gatk4spark/markduplicates)

nf-core-lint (hamronization/abricate)

nf-test (star/align, singularity)

nf-test (tcoffee/align, conda)

nf-core-lint (muscle5/super5)

nf-test (star/align, docker)

nf-test (umitools/extract, docker)

nf-test (subworkflows/bam_create_som_pon_gatk, singularity)

nf-core-lint (hamronization/deeparg)

nf-core-lint (hamronization/summarize)

nf-test (subworkflows/bam_create_som_pon_gatk, docker)

nf-core-lint (quartonotebook)

nf-core-lint (multiqc)

nf-core-lint (propr/propr)

nf-core-lint (mtmalign/align)

nf-core-lint (mafft)

nf-core-lint (rseqc/tin)

nf-core-lint (rseqc/bamstat)

nf-core-lint (samtools/ampliconclip)

nf-core-lint (pyrodigal)

nf-core-lint (salmon/index)

nf-test (trimgalore, singularity)

nf-core-lint (rsem/preparereference)

nf-core-lint (rhocall/viz)

nf-core-lint (rsem/calculateexpression)

nf-core-lint (rseqc/readdistribution)

nf-test (star/genomegenerate, docker)

nf-core-lint (samtools/calmd)

nf-core-lint (salmon/quant)

nf-core-lint (samtools/coverage)

nf-test (star/genomegenerate, singularity)

nf-test (tximeta/tximport, singularity)

nf-core-lint (samtools/collate)

nf-core-lint (samtools/faidx)

nf-core-lint (samtools/bam2fq)

nf-core-lint (samtools/collatefastq)

nf-core-lint (samtools/convert)

nf-core-lint (samtools/fasta)

nf-core-lint (samtools/flagstat)

nf-core-lint (samtools/fastq)

nf-core-lint (samtools/getrg)

nf-core-lint (samtools/mpileup)

nf-core-lint (samtools/depth)

nf-core-lint (samtools/merge)

nf-core-lint (samtools/reheader)

nf-core-lint (samtools/fixmate)

nf-core-lint (samtools/import)

nf-test (tximeta/tximport, docker)

nf-core-lint (samtools/index)

nf-core-lint (samtools/idxstats)

nf-core-lint (samtools/cat)

nf-core-lint (samtools/sort)

nf-core-lint (samtools/stats)

nf-core-lint (sentieon/applyvarcal)

nf-core-lint (sentieon/bwamem)

nf-core-lint (samtools/markdup)

nf-core-lint (samtools/view)

nf-core-lint (sentieon/bwaindex)

nf-test (subworkflows/fastq_fastqc_umitools_trimgalore, conda)

nf-core-lint (sentieon/dedup)

nf-core-lint (sentieon/readwriter)

nf-core-lint (sentieon/dnascope)

nf-core-lint (sentieon/tnfilter)

nf-test (star/align, conda)

nf-core-lint (samtools/dict)

nf-core-lint (sentieon/gvcftyper)

nf-core-lint (sentieon/dnamodelapply)

nf-core-lint (sentieon/datametrics)

nf-test (trimgalore, conda)

nf-test (samtools/index, conda)

nf-core-lint (sentieon/tnscope)

nf-core-lint (sentieon/haplotyper)

nf-core-lint (sentieon/tnhaplotyper2)

nf-core-lint (seqkit/fx2tab)

nf-core-lint (seqkit/concat)

nf-test (umitools/extract, singularity)

nf-test (subworkflows/bam_create_som_pon_gatk, conda)

nf-core-lint (sentieon/varcal)

nf-core-lint (star/align)

nf-core-lint (sentieon/wgsmetrics)

nf-core-lint (stringtie/merge)

nf-core-lint (subworkflows/bam_create_som_pon_gatk)

nf-core-lint (stringtie/stringtie)

nf-core-lint (star/genomegenerate)

nf-core-lint (subworkflows/bam_rseqc)

nf-core-lint (subworkflows/bam_sort_stats_samtools)

nf-core-lint (subworkflows/bam_dedup_stats_samtools_umitools)

nf-core-lint (sortmerna)

nf-core-lint (subread/featurecounts)

nf-core-lint (seqkit/tab2fx)

nf-core-lint (subworkflows/fastq_fastqc_umitools_trimgalore)

nf-core-lint (tcoffee/align)

nf-core-lint (subworkflows/preprocess_rnaseq)

nf-core-lint (trimgalore)

nf-core-lint (subworkflows/bam_markduplicates_picard)

nf-core-lint (tcoffee/alncompare)

nf-core-lint (subworkflows/bam_stats_samtools)

nf-core-lint (tcoffee/irmsd)

nf-core-lint (subworkflows/utils_nfcore_pipeline)

nf-core-lint (svdb/merge)

nf-core-lint (ucsc/bedclip)

nf-core-lint (ucsc/bedgraphtobigwig)

nf-core-lint (wfmash)

nf-core-lint (umitools/prepareforrsem)

nf-core-lint (summarizedexperiment/summarizedexperiment)

nf-core-lint (umitools/extract)

nf-test (subworkflows/bam_stats_samtools, conda)

nf-core-lint (tximeta/tximport)

nf-test (star/genomegenerate, conda)

nf-test (umitools/extract, conda)

pytest (samtools/coverage, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/github-script@v6. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (samtools/dict, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/github-script@v6. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (samtools/coverage, docker)

pytest (samtools/coverage, conda)

pytest (samtools/collatefastq, singularity)

pytest (samtools/depth, docker)

pytest (samtools/dict, conda)

pytest (samtools/depth, singularity)

nf-test (samtools/stats, conda)

pytest (samtools/getrg, conda)

pytest (samtools/fasta, docker)

pytest (samtools/dict, singularity)

pytest (samtools/collatefastq, docker)

pytest (samtools/import, singularity)

pytest (samtools/getrg, docker)

pytest (samtools/getrg, singularity)

pytest (samtools/fasta, conda)

pytest (samtools/faidx, singularity)

pytest (samtools/fasta, singularity)

pytest (samtools/import, docker)

pytest (samtools/depth, conda)

pytest (samtools/reheader, conda)

pytest (sentieon/bwaindex, docker)

pytest (samtools/markdup, singularity)

pytest (samtools/faidx, docker)

pytest (sentieon/datametrics, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (samtools/reheader, docker)

pytest (samtools/markdup, docker)

pytest (sentieon/applyvarcal, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (samtools/collatefastq, conda)

pytest (gsea/gsea, docker)

pytest (sentieon/bwamem, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (samtools/import, conda)

pytest (sentieon/applyvarcal, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (samtools/reheader, singularity)

pytest (sentieon/bwamem, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/datametrics, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/dnamodelapply, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/dedup, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (gsea/gsea, singularity)

pytest (sentieon/bwaindex, singularity)

pytest (sentieon/dedup, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (gsea/gsea, conda)

pytest (samtools/faidx, conda)

nf-test (samtools/merge, singularity)

pytest (sentieon/dnamodelapply, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (samtools/markdup, conda)

pytest (sentieon/dnascope, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/readwriter, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/gvcftyper, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/gvcftyper, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/dnascope, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/haplotyper, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/haplotyper, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/wgsmetrics, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/wgsmetrics, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (subworkflows/utils_nfcore_pipeline, conda)

pytest (sentieon/varcal, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/tnfilter, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (seqkit/fx2tab, singularity)

pytest (sentieon/tnscope, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (seqkit/fx2tab, conda)

nf-test (antismash/antismashlite, singularity)

pytest (subworkflows/utils_nfcore_pipeline, docker)

pytest (sentieon/readwriter, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (seqkit/fx2tab, docker)

pytest (subworkflows/utils_nfcore_pipeline, singularity)

pytest (seqkit/tab2fx, docker)

pytest (sentieon/tnscope, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/varcal, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

nf-test (summarizedexperiment/summarizedexperiment, conda)

pytest (sentieon/tnfilter, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (seqkit/tab2fx, singularity)

pytest (seqkit/tab2fx, conda)

nf-test (antismash/antismashlite, docker)

nf-test (tximeta/tximport, conda)

pytest (sentieon/tnhaplotyper2, singularity)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, eWaterCycle/setup-apptainer@main, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

pytest (sentieon/tnhaplotyper2, docker)

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/setup-python@v4, actions/setup-java@v3, nf-core/setup-nextflow@v1, conda-incubator/setup-miniconda@v2, actions/upload-artifact@v3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

nf-test (antismash/antismashlite, conda)

nf-test (antismash/antismashlitedownloaddatabases, conda)

You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 50 MB

nf-test (antismash/antismashlitedownloaddatabases, docker)

You are running out of disk space. The runner will stop working when the machine runs out of disk space. Free space left: 22 MB

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Name	Size
logs-docker- Expired	1.77 GB
logs-singularity- Expired	1.77 GB

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nf-test to FASTQ_FASTQC_UMITOOLS_TRIMGALORE and pin cutadapt in trimgalore #6559

Summary

nf-test to FASTQ_FASTQC_UMITOOLS_TRIMGALORE and pin cutadapt in trimgalore #6559

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