Added new module for Toulligqc (#5131) #3
jennylsmithtest.yml
on: push
Matrix: nf-test
Matrix: nf-core-lint
Matrix: pytest
confirm-pass
0s
Annotations
354 errors and 3 warnings
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nf-test (bcftools/filter, singularity)
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nf-test (plink/ld, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (strelka/somatic, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (plink/epistasis, docker)
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nf-test (isoseq3/tag, conda)
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nf-test (plink/epistasis, conda)
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nf-test (kaiju/mergeoutputs, docker)
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nf-test (isoseq3/tag, docker)
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nf-test (kaiju/mergeoutputs, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (toulligqc, conda)
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nf-test (kalign/align, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (celesta, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (toulligqc, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kaiju/mergeoutputs, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (dragmap/align, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (toulligqc, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kalign/align, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (dragmap/align, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (dragmap/align, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kalign/align, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (strelka/somatic, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (strelka/germline, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_align_dna, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_align_dna, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (strelka/germline, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (celesta, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kraken2/kraken2, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (strelka/somatic, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (bamclipper, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (openms/peptideindexer, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (krakentools/extractkrakenreads, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kraken2/build, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (deepvariant, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (openms/idmerger, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kraken2/build, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (openms/idmerger, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (openms/peptideindexer, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (openms/idmerger, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (circularmapper/circulargenerator, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (circularmapper/circulargenerator, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (wittyer, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (openms/peptideindexer, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (circularmapper/circulargenerator, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (wittyer, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_align_dna, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_align_mapad, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_align_mapad, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_taxonomic_profile_metaphlan, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/bam_markduplicates_picard, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/bam_markduplicates_picard, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/bam_markduplicates_picard, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_taxonomic_profile_metaphlan, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (quartonotebook, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_align_mapad, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (president, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (subworkflows/fastq_taxonomic_profile_metaphlan, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (cnvkit/batch, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kraken2/kraken2, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (quartonotebook, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kraken2/kraken2, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (deepvariant, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-test (kraken2/build, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (mosdepth)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (popscle/dscpileup)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (manta/somatic)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (manta/tumoronly)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (molkartgarage/clahe)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (crabz/compress)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (bakta/bakta)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gtdbtk/classifywf)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (crabz/decompress)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (bamstats/generalstats)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (pretextmap)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (islandpath)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/addorreplacereadgroups)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (mygene)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (hmmer/hmmsearch)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (scimap/spatiallda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (taxonkit/name2taxid)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/combinegvcfs)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/estimatelibrarycomplexity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (controlfreec/assesssignificance)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/svcluster)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (controlfreec/makegraph2)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (bcftools/stats)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (learnmsa/align)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/svannotate)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (genomescope2)
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nf-core-lint (leviosam2/index)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (nanofilt)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (manta/germline)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (igvreports)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (vcftools)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (rgi/main)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (leviosam2/lift)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (bcftools/filter)
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nf-core-lint (cellranger/mkgtf)
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nf-core-lint (rgi/cardannotation)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (cellranger/multi)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (cellranger/count)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (cellranger/mkvdjref)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (controlfreec/makegraph)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gecco/run)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (plink/epistasis)
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nf-core-lint (cellranger/vdj)
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nf-core-lint (isoseq3/tag)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (plink/ld)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (plink/fastepistasis)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (bamclipper)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (cnvkit/batch)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (decoupler/decoupler)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (strelka/somatic)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (krakentools/extractkrakenreads)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (strelka/germline)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (president)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (kraken2/build)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (deepvariant)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (circularmapper/circulargenerator)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (controlfreec/freec)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (cellranger/mkref)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (kraken2/kraken2)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (meryl/unionsum)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (meryl/histogram)
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nf-core-lint (picard/markduplicates)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (meryl/count)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (plink/gwas)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (bases2fastq)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (tiddit/sv)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (ensemblvep/vep)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (kallistobustools/count)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (picard/addorreplacereadgroups)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (svtyper/svtypersso)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (bwamem2/mem)
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nf-core-lint (tcoffee/tcs)
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nf-core-lint (metamaps/mapdirectly)
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nf-core-lint (toulligqc)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (ensemblvep/download)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (subworkflows/bam_markduplicates_picard)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (celesta)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (subworkflows/fastq_align_dna)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (subworkflows/fastq_taxonomic_profile_metaphlan)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/germlinecnvcaller)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (subworkflows/vcf_phase_shapeit5)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/postprocessgermlinecnvcalls)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (ashlar)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (shapeit5/ligate)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/cnnscorevariants)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (openms/idmerger)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (gatk4/determinegermlinecontigploidy)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (openms/peptideindexer)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (quartonotebook)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (dragmap/align)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (kaiju/mergeoutputs)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (ashlar, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (wittyer)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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nf-core-lint (kalign/align)
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nf-core-lint (subworkflows/fastq_align_mapad)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (ashlar, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (gatk4/cnnscorevariants, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (subworkflows/vcf_phase_shapeit5, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (gatk4/cnnscorevariants, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (gatk4/postprocessgermlinecnvcalls, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (ashlar, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (subworkflows/vcf_phase_shapeit5, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (gatk4/germlinecnvcaller, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (gatk4/germlinecnvcaller, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (gatk4/determinegermlinecontigploidy, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (subworkflows/vcf_phase_shapeit5, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (shapeit5/ligate, conda)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (shapeit5/ligate, docker)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (gatk4/postprocessgermlinecnvcalls, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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pytest (shapeit5/ligate, singularity)
Canceling since a higher priority waiting request for 'Run tests-refs/heads/master' exists
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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/.
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pytest-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/.
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pre-commit
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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