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Fix for #4692 added double quotes for find command in gtdbtk/classify… #1

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Fix for #4692 added double quotes for find command in gtdbtk/classify…

Fix for #4692 added double quotes for find command in gtdbtk/classify… #1

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Job Run time
pre-commit
53s
prettier
32s
editorconfig
8s
nf-test-changes
8s
pytest-changes
5s
nf-core-lint (angsd/contamination)
1s
nf-core-lint (bases2fastq)
1s
nf-core-lint (bowtie/align)
1s
nf-core-lint (cellranger/mkvdjref)
1s
pytest (angsd/contamination, conda)
1s
nf-core-lint (cellrangerarc/count)
1s
pytest (angsd/contamination, docker)
1s
nf-core-lint (cellrangerarc/mkfastq)
1s
pytest (angsd/contamination, singularity)
1s
nf-core-lint (cellrangerarc/mkgtf)
1s
pytest (bases2fastq, docker)
1s
nf-core-lint (cellrangerarc/mkref)
1s
pytest (bowtie/align, conda)
1s
nf-core-lint (cnvkit/access)
1s
pytest (bowtie/align, docker)
1s
nf-core-lint (cnvkit/antitarget)
1s
pytest (bowtie/align, singularity)
1s
nf-core-lint (cnvkit/batch)
1s
pytest (cellranger/mkvdjref, docker)
1s
nf-core-lint (cnvkit/call)
1s
pytest (cellranger/mkvdjref, singularity)
1s
nf-core-lint (cnvkit/export)
1s
pytest (cellrangerarc/count, docker)
1s
nf-core-lint (cnvkit/genemetrics)
1s
pytest (cellrangerarc/count, singularity)
1s
nf-core-lint (cnvkit/reference)
1s
pytest (cellrangerarc/mkfastq, docker)
1s
nf-core-lint (cnvkit/target)
1s
pytest (cellrangerarc/mkfastq, singularity)
1s
nf-core-lint (custom/tabulartogseacls)
1s
pytest (cellrangerarc/mkgtf, docker)
1s
nf-core-lint (deeparg/downloaddata)
1s
pytest (cellrangerarc/mkgtf, singularity)
1s
nf-core-lint (deeparg/predict)
1s
pytest (cellrangerarc/mkref, docker)
1s
nf-core-lint (faqcs)
1s
pytest (cellrangerarc/mkref, singularity)
1s
nf-core-lint (fqtk)
1s
pytest (cnvkit/access, conda)
1s
nf-core-lint (gprofiler2/gost)
1s
pytest (cnvkit/access, docker)
1s
nf-core-lint (gtdbtk/classifywf)
1s
pytest (cnvkit/access, singularity)
1s
pytest (cnvkit/antitarget, conda)
1s
pytest (cnvkit/antitarget, docker)
1s
nf-core-lint (manta/convertinversion)
1s
pytest (cnvkit/antitarget, singularity)
1s
nf-core-lint (motus/profile)
1s
pytest (cnvkit/batch, conda)
1s
nf-core-lint (ncbigenomedownload)
1s
pytest (cnvkit/batch, docker)
1s
pytest (cnvkit/batch, singularity)
1s
nf-core-lint (parabricks/deepvariant)
1s
pytest (cnvkit/call, conda)
1s
nf-core-lint (parabricks/fq2bam)
1s
pytest (cnvkit/call, docker)
1s
nf-core-lint (parabricks/genotypegvcf)
1s
pytest (cnvkit/call, singularity)
1s
nf-core-lint (parabricks/haplotypecaller)
1s
pytest (cnvkit/export, conda)
1s
nf-core-lint (parabricks/indexgvcf)
1s
pytest (cnvkit/export, docker)
1s
nf-core-lint (parabricks/mutectcaller)
1s
pytest (cnvkit/export, singularity)
1s
nf-core-lint (pretextsnapshot)
1s
pytest (cnvkit/genemetrics, conda)
1s
nf-core-lint (purgedups/calcuts)
1s
pytest (cnvkit/genemetrics, docker)
1s
nf-core-lint (purgedups/purgedups)
1s
pytest (cnvkit/genemetrics, singularity)
1s
nf-core-lint (samtools/collatefastq)
1s
nf-core-lint (samtools/coverage)
1s
pytest (cnvkit/reference, conda)
1s
pytest (cnvkit/reference, docker)
1s
nf-core-lint (samtools/depth)
1s
pytest (cnvkit/reference, singularity)
1s
nf-core-lint (samtools/dict)
1s
pytest (cnvkit/target, conda)
1s
nf-core-lint (samtools/faidx)
1s
pytest (cnvkit/target, docker)
1s
nf-core-lint (samtools/fasta)
1s
pytest (cnvkit/target, singularity)
1s
nf-core-lint (samtools/getrg)
1s
pytest (custom/tabulartogseacls, conda)
1s
nf-core-lint (samtools/import)
1s
pytest (custom/tabulartogseacls, docker)
1s
nf-core-lint (samtools/markdup)
1s
pytest (custom/tabulartogseacls, singularity)
1s
nf-core-lint (samtools/reheader)
1s
pytest (deeparg/downloaddata, conda)
1s
nf-core-lint (sgdemux)
1s
pytest (deeparg/downloaddata, docker)
1s
nf-core-lint (shinyngs/app)
1s
pytest (deeparg/downloaddata, singularity)
1s
nf-core-lint (shinyngs/staticdifferential)
1s
pytest (deeparg/predict, conda)
1s
nf-core-lint (shinyngs/staticexploratory)
1s
pytest (deeparg/predict, docker)
1s
nf-core-lint (shinyngs/validatefomcomponents)
1s
pytest (deeparg/predict, singularity)
1s
nf-core-lint (subworkflows/bam_markduplicates_samtools)
1s
pytest (faqcs, conda)
1s
nf-core-lint (subworkflows/utils_nfcore_pipeline)
1s
pytest (faqcs, docker)
1s
nf-core-lint (umitools/dedup)
1s
pytest (faqcs, singularity)
1s
nf-core-lint (umitools/group)
1s
pytest (fqtk, conda)
1s
nf-core-lint (openms/idripper)
1s
pytest (fqtk, docker)
1s
nf-core-lint (openms/idscoreswitcher)
1s
pytest (fqtk, singularity)
1s
nf-core-lint (openms/decoydatabase)
1s
pytest (gprofiler2/gost, conda)
1s
nf-core-lint (cat/cat)
1s
pytest (gprofiler2/gost, docker)
1s
nf-core-lint (cat/fastq)
1s
pytest (gprofiler2/gost, singularity)
1s
nf-core-lint (xz/decompress)
1s
pytest (gtdbtk/classifywf, conda)
1s
nf-core-lint (xz/compress)
1s
pytest (gtdbtk/classifywf, docker)
1s
nf-core-lint (ganon/buildcustom)
1s
pytest (gtdbtk/classifywf, singularity)
1s
nf-core-lint (ganon/report)
1s
pytest (manta/convertinversion, docker)
1s
nf-core-lint (ganon/table)
1s
pytest (manta/convertinversion, singularity)
1s
nf-core-lint (ganon/classify)
1s
pytest (motus/profile, conda)
1s
nf-core-lint (bedtools/complement)
1s
pytest (motus/profile, docker)
1s
nf-core-lint (bedtools/coverage)
1s
pytest (motus/profile, singularity)
1s
nf-core-lint (bedtools/closest)
1s
pytest (ncbigenomedownload, conda)
1s
nf-core-lint (bedtools/bamtobed)
1s
pytest (ncbigenomedownload, docker)
1s
nf-core-lint (bedtools/genomecov)
1s
pytest (ncbigenomedownload, singularity)
1s
nf-core-lint (sratools/prefetch)
1s
pytest (parabricks/deepvariant, docker)
1s
nf-core-lint (sratools/fasterqdump)
1s
pytest (parabricks/deepvariant, singularity)
1s
nf-core-lint (vcfanno)
1s
pytest (parabricks/fq2bam, docker)
1s
nf-core-lint (multiqc)
1s
pytest (parabricks/fq2bam, singularity)
1s
nf-core-lint (qualimap/bamqccram)
1s
pytest (parabricks/genotypegvcf, docker)
1s
nf-core-lint (qualimap/rnaseq)
1s
pytest (parabricks/genotypegvcf, singularity)
1s
nf-core-lint (qualimap/bamqc)
1s
pytest (parabricks/haplotypecaller, docker)
1s
nf-core-lint (samtools/sort)
1s
pytest (parabricks/haplotypecaller, singularity)
1s
nf-core-lint (samtools/convert)
1s
pytest (parabricks/indexgvcf, docker)
1s
nf-core-lint (samtools/cat)
1s
pytest (parabricks/indexgvcf, singularity)
1s
nf-core-lint (samtools/index)
1s
pytest (parabricks/mutectcaller, docker)
1s
nf-core-lint (samtools/collate)
1s
pytest (parabricks/mutectcaller, singularity)
1s
nf-core-lint (samtools/flagstat)
1s
pytest (pretextsnapshot, conda)
1s
nf-core-lint (samtools/merge)
1s
pytest (pretextsnapshot, docker)
1s
nf-core-lint (samtools/mpileup)
1s
pytest (pretextsnapshot, singularity)
1s
nf-core-lint (samtools/fastq)
1s
pytest (purgedups/calcuts, conda)
1s
nf-core-lint (samtools/stats)
1s
pytest (purgedups/calcuts, docker)
1s
nf-core-lint (samtools/view)
1s
pytest (purgedups/calcuts, singularity)
1s
nf-core-lint (samtools/idxstats)
1s
pytest (purgedups/purgedups, conda)
1s
nf-core-lint (samtools/bam2fq)
1s
pytest (purgedups/purgedups, docker)
1s
nf-core-lint (samtools/calmd)
1s
pytest (purgedups/purgedups, singularity)
1s
nf-core-lint (samtools/ampliconclip)
1s
pytest (samtools/collatefastq, conda)
1s
nf-core-lint (samtools/fixmate)
1s
pytest (samtools/collatefastq, docker)
1s
nf-core-lint (famsa/guidetree)
1s
pytest (samtools/collatefastq, singularity)
1s
nf-core-lint (cobs/compactconstruct)
1s
pytest (samtools/coverage, conda)
1s
nf-core-lint (cobs/classicconstruct)
1s
pytest (samtools/coverage, docker)
1s
nf-core-lint (mtmalign/align)
1s
pytest (samtools/coverage, singularity)
1s
nf-core-lint (proteinortho)
1s
pytest (samtools/depth, conda)
1s
pytest (samtools/depth, docker)
1s
pytest (samtools/depth, singularity)
1s
nf-core-lint (filtlong)
1s
pytest (samtools/dict, conda)
1s
nf-core-lint (vcf2cytosure)
1s
pytest (samtools/dict, docker)
1s
nf-core-lint (custom/catadditionalfasta)
1s
pytest (samtools/dict, singularity)
1s
nf-core-lint (custom/dumpsoftwareversions)
1s
pytest (samtools/faidx, conda)
1s
nf-core-lint (custom/sratoolsncbisettings)
1s
pytest (samtools/faidx, docker)
1s
nf-core-lint (rseqc/junctionsaturation)
1s
pytest (samtools/faidx, singularity)
1s
nf-core-lint (rseqc/innerdistance)
1s
pytest (samtools/fasta, conda)
1s
nf-core-lint (rseqc/readdistribution)
1s
pytest (samtools/fasta, docker)
1s
nf-core-lint (rseqc/bamstat)
1s
pytest (samtools/fasta, singularity)
1s
nf-core-lint (rseqc/junctionannotation)
1s
pytest (samtools/getrg, conda)
1s
nf-core-lint (rseqc/readduplication)
1s
pytest (samtools/getrg, docker)
1s
nf-core-lint (rseqc/inferexperiment)
1s
pytest (samtools/getrg, singularity)
1s
nf-core-lint (rseqc/tin)
1s
pytest (samtools/import, conda)
1s
nf-core-lint (fastqc)
1s
pytest (samtools/import, docker)
1s
nf-core-lint (gatk4spark/applybqsr)
1s
pytest (samtools/import, singularity)
1s
nf-core-lint (gatk4spark/markduplicates)
1s
pytest (samtools/markdup, conda)
1s
nf-core-lint (dragmap/hashtable)
1s
pytest (samtools/markdup, docker)
1s
nf-core-lint (dragmap/align)
1s
pytest (samtools/markdup, singularity)
1s
nf-core-lint (pigz/compress)
1s
pytest (samtools/reheader, conda)
1s
nf-core-lint (blast/tblastn)
1s
pytest (samtools/reheader, docker)
1s
nf-core-lint (blast/blastn)
1s
pytest (samtools/reheader, singularity)
1s
nf-core-lint (picard/extractfingerprint)
1s
pytest (sgdemux, conda)
1s
nf-core-lint (checkm2/predict)
1s
pytest (sgdemux, docker)
1s
nf-core-lint (checkm2/databasedownload)
1s
pytest (sgdemux, singularity)
1s
nf-core-lint (pyrodigal)
1s
pytest (shinyngs/app, conda)
1s
nf-core-lint (diamond/makedb)
1s
pytest (shinyngs/app, docker)
1s
nf-core-lint (diamond/blastp)
1s
pytest (shinyngs/app, singularity)
1s
nf-core-lint (diamond/blastx)
1s
pytest (shinyngs/staticdifferential, conda)
1s
nf-core-lint (fastp)
1s
pytest (shinyngs/staticdifferential, docker)
1s
nf-core-lint (agrvate)
1s
pytest (shinyngs/staticdifferential, singularity)
1s
nf-core-lint (seqkit/sort)
1s
pytest (shinyngs/staticexploratory, conda)
1s
nf-core-lint (seqkit/seq)
1s
pytest (shinyngs/staticexploratory, docker)
1s
nf-core-lint (minimap2/align)
1s
pytest (shinyngs/staticexploratory, singularity)
1s
pytest (shinyngs/validatefomcomponents, conda)
1s
pytest (shinyngs/validatefomcomponents, docker)
1s
nf-core-lint (spaceranger/mkgtf)
1s
pytest (shinyngs/validatefomcomponents, singularity)
1s
nf-core-lint (spaceranger/count)
1s
pytest (subworkflows/bam_markduplicates_samtools, conda)
1s
nf-core-lint (spaceranger/mkref)
1s
pytest (subworkflows/bam_markduplicates_samtools, docker)
1s
nf-core-lint (deepbgc/download)
1s
pytest (subworkflows/bam_markduplicates_samtools, singularity)
1s
nf-core-lint (deepbgc/pipeline)
1s
pytest (subworkflows/utils_nfcore_pipeline, conda)
1s
nf-core-lint (star/align)
1s
pytest (subworkflows/utils_nfcore_pipeline, docker)
1s
nf-core-lint (star/genomegenerate)
1s
pytest (subworkflows/utils_nfcore_pipeline, singularity)
1s
nf-core-lint (freebayes)
1s
pytest (umitools/dedup, conda)
1s
nf-core-lint (gffread)
1s
pytest (umitools/dedup, docker)
1s
nf-core-lint (abricate/run)
46s
nf-core-lint (tiddit/cov)
1s
nf-core-lint (truvari/consistency)
1s
pytest (umitools/dedup, singularity)
1s
nf-core-lint (truvari/segment)
1s
pytest (umitools/group, conda)
1s
nf-core-lint (tidk/search)
1s
pytest (umitools/group, docker)
1s
nf-core-lint (tidk/explore)
1s
pytest (umitools/group, singularity)
1s
nf-core-lint (tidk/plot)
1s
nf-core-lint (pharokka/installdatabases)
1s
nf-core-lint (pharokka/pharokka)
1s
nf-core-lint (bowtie2/align)
1s
nf-core-lint (bacphlip)
1s
nf-core-lint (bwamem2/mem)
1s
nf-core-lint (allelecounter)
1s
nf-core-lint (agat/sqstatbasic)
1s
nf-core-lint (agat/convertspgff2gtf)
38s
nf-core-lint (agat/spaddintrons)
12s
nf-core-lint (agat/spstatistics)
1s
nf-core-lint (vcf2db)
1s
nf-core-lint (ampir)
1s
nf-core-lint (gatk4/baserecalibrator)
1s
nf-core-lint (gatk4/applybqsr)
1s
nf-core-lint (gatk4/markduplicates)
1s
nf-core-lint (gatk4/annotateintervals)
1s
nf-core-lint (prokka)
1s
nf-core-lint (vsearch/cluster)
1s
nf-core-lint (foldcomp/decompress)
1s
nf-core-lint (foldcomp/compress)
1s
nf-core-lint (mash/sketch)
1s
nf-core-lint (mash/screen)
1s
nf-core-lint (bwa/sampe)
1s
nf-core-lint (bwa/mem)
1s
nf-core-lint (bwa/samse)
1s
nf-core-lint (umitools/extract)
1s
nf-core-lint (abritamr/run)
42s
nf-core-lint (sortmerna)
1s
nf-core-lint (freyja/variants)
1s
nf-core-lint (freyja/update)
1s
nf-core-lint (freyja/boot)
1s
nf-core-lint (freyja/demix)
1s
nf-core-lint (aria2)
1s
nf-core-lint (presto/filterseq)
1s
nf-core-lint (narfmap/hashtable)
1s
nf-core-lint (narfmap/align)
1s
nf-core-lint (gt/gff3)
1s
nf-core-lint (untar)
1s
nf-core-lint (hmmcopy/generatemap)
1s
nf-core-lint (hmmcopy/gccounter)
1s
nf-core-lint (hmmcopy/readcounter)
1s
nf-core-lint (hmmcopy/mapcounter)
1s
nf-core-lint (deepcell/mesmer)
1s
nf-core-lint (ariba/run)
1s
nf-core-lint (tcoffee/alncompare)
1s
nf-core-lint (tcoffee/irmsd)
1s
nf-core-lint (kraken2/kraken2)
1s
nf-core-lint (mindagap/mindagap)
1s
nf-core-lint (adapterremoval)
44s
nf-core-lint (porechop/porechop)
1s
nf-core-lint (subworkflows/utils_nfvalidation_plugin)
1s
nf-core-lint (subworkflows/bam_dedup_stats_samtools_umitools)
1s
nf-core-lint (subworkflows/fasta_explore_search_plot_tidk)
1s
nf-core-lint (subworkflows/fastq_download_prefetch_fasterqdump_sratools)
1s
nf-core-lint (subworkflows/fastq_subsample_fq_salmon)
1s
nf-core-lint (subworkflows/bam_sort_stats_samtools)
1s
nf-core-lint (subworkflows/utils_nfcore_pipeline)
1s
nf-core-lint (subworkflows/bam_markduplicates_picard)
1s
nf-core-lint (subworkflows/fastq_fastqc_umitools_fastp)
1s
nf-core-lint (subworkflows/bam_stats_samtools)
1s
nf-core-lint (subworkflows/bam_rseqc)
1s
confirm-pass
1s
10m 40s