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run nf-core lint on trimgalore (#5129) #24

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run nf-core lint on trimgalore (#5129)

run nf-core lint on trimgalore (#5129) #24

Run time

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Job Run time
pre-commit
44s
nf-test-changes
5s
prettier
41s
editorconfig
10s
pytest-changes
4s
pytest (bases2fastq, docker)
1s
pytest (cellrangerarc/count, docker)
1s
pytest (cellrangerarc/count, singularity)
1s
pytest (fqtk, conda)
1s
pytest (fqtk, docker)
1s
pytest (fqtk, singularity)
1s
pytest (gatk/unifiedgenotyper, conda)
1s
pytest (gatk/unifiedgenotyper, docker)
1s
pytest (gatk/unifiedgenotyper, singularity)
1s
pytest (minimap2/index, conda)
1s
pytest (minimap2/index, docker)
1s
pytest (minimap2/index, singularity)
1s
pytest (sgdemux, conda)
1s
pytest (sgdemux, docker)
1s
pytest (sgdemux, singularity)
1s
pytest (subworkflows/utils_nextflow_pipeline, conda)
1s
pytest (subworkflows/utils_nextflow_pipeline, docker)
1s
pytest (subworkflows/utils_nextflow_pipeline, singularity)
1s
pytest (subworkflows/utils_nfcore_pipeline, conda)
1s
pytest (subworkflows/utils_nfcore_pipeline, docker)
1s
pytest (subworkflows/utils_nfcore_pipeline, singularity)
1s
nf-core-lint (bases2fastq)
1s
nf-core-lint (cellrangerarc/count)
1s
nf-core-lint (fqtk)
1s
nf-core-lint (gatk/unifiedgenotyper)
1s
nf-core-lint (minimap2/index)
1s
nf-core-lint (sgdemux)
1s
nf-core-lint (subworkflows/utils_nextflow_pipeline)
1s
nf-core-lint (subworkflows/utils_nfcore_pipeline)
1s
nf-core-lint (subworkflows/fastq_fastqc_umitools_trimgalore)
1s
nf-core-lint (subworkflows/fastq_align_bwa)
1s
nf-core-lint (subworkflows/utils_nfvalidation_plugin)
1s
nf-core-lint (subworkflows/utils_nextflow_pipeline)
1s
nf-core-lint (subworkflows/bam_sort_stats_samtools)
1s
nf-core-lint (subworkflows/utils_nfcore_pipeline)
1s
nf-core-lint (subworkflows/fastq_download_prefetch_fasterqdump_sratools)
1s
nf-core-lint (subworkflows/fastq_align_star)
1s
nf-core-lint (subworkflows/fastq_align_dna)
1s
nf-core-lint (subworkflows/fastq_align_hisat2)
1s
nf-core-lint (summarizedexperiment/summarizedexperiment)
1s
nf-core-lint (gffread)
1s
nf-core-lint (bedtools/genomecov)
1s
nf-core-lint (custom/sratoolsncbisettings)
1s
nf-core-lint (svanalyzer/svbenchmark)
1s
nf-core-lint (bwa/mem)
1s
nf-core-lint (mtmalign/align)
1s
nf-core-lint (bbmap/bbsplit)
1s
nf-core-lint (umicollapse)
1s
nf-core-lint (kraken2/kraken2)
1s
nf-core-lint (krakentools/extractkrakenreads)
1s
nf-core-lint (resfinder/run)
1s
nf-core-lint (seqtk/seq)
1s
nf-core-lint (seqtk/sample)
1s
nf-core-lint (seqtk/mergepe)
1s
nf-core-lint (seqtk/cutn)
1s
nf-core-lint (seqtk/subseq)
1s
nf-core-lint (seqtk/rename)
1s
nf-core-lint (geofetch)
1s
nf-core-lint (happy/prepy)
1s
nf-core-lint (cutadapt)
1s
nf-core-lint (kallistobustools/count)
1s
nf-core-lint (kallistobustools/ref)
1s
nf-core-lint (picard/crosscheckfingerprints)
1s
nf-core-lint (mmseqs/createtsv)
1s
nf-core-lint (minimap2/align)
1s
nf-core-lint (tcoffee/align)
1s
nf-core-lint (ribotish/quality)
1s
nf-core-lint (ribotish/predict)
1s
nf-core-lint (umitools/dedup)
1s
nf-core-lint (umitools/prepareforrsem)
1s
nf-core-lint (umitools/extract)
1s
nf-core-lint (tximeta/tximport)
1s
nf-test (subworkflows/fastq_fastqc_umitools_trimgalore, conda)
1s
nf-core-lint (preseq/lcextrap)
1s
nf-test (subworkflows/fastq_fastqc_umitools_trimgalore, docker)
1s
nf-core-lint (sratools/fasterqdump)
1s
nf-test (subworkflows/fastq_fastqc_umitools_trimgalore, singularity)
1s
nf-core-lint (sratools/prefetch)
1s
nf-test (subworkflows/fastq_align_bwa, conda)
1s
nf-core-lint (cellranger/count)
1s
nf-test (subworkflows/fastq_align_bwa, docker)
1s
nf-core-lint (untar)
1s
nf-test (subworkflows/fastq_align_bwa, singularity)
1s
nf-core-lint (trust4)
1s
nf-test (subworkflows/utils_nfvalidation_plugin, conda)
1s
nf-core-lint (glimpse2/phase)
1s
nf-test (subworkflows/utils_nfvalidation_plugin, docker)
1s
nf-core-lint (glimpse2/chunk)
1s
nf-test (subworkflows/utils_nfvalidation_plugin, singularity)
1s
nf-core-lint (glimpse2/splitreference)
1s
nf-test (subworkflows/utils_nextflow_pipeline, conda)
1s
nf-test (subworkflows/utils_nextflow_pipeline, docker)
1s
nf-core-lint (gatk4/genomicsdbimport)
1s
nf-test (subworkflows/utils_nextflow_pipeline, singularity)
1s
nf-core-lint (stringtie/stringtie)
1s
nf-test (subworkflows/bam_sort_stats_samtools, conda)
1s
nf-core-lint (tabix/bgzip)
1s
nf-test (subworkflows/bam_sort_stats_samtools, docker)
1s
nf-core-lint (tabix/tabix)
1s
nf-test (subworkflows/bam_sort_stats_samtools, singularity)
1s
nf-core-lint (tabix/bgziptabix)
1s
nf-test (subworkflows/utils_nfcore_pipeline, conda)
1s
nf-core-lint (trimgalore)
1s
nf-test (subworkflows/utils_nfcore_pipeline, docker)
1s
nf-core-lint (ribotricer/prepareorfs)
1s
nf-test (subworkflows/utils_nfcore_pipeline, singularity)
1s
nf-core-lint (ribotricer/detectorfs)
1s
nf-test (subworkflows/fastq_download_prefetch_fasterqdump_sratools, conda)
1s
nf-core-lint (dupradar)
1s
nf-test (subworkflows/fastq_download_prefetch_fasterqdump_sratools, docker)
1s
nf-core-lint (bakta/bakta)
1s
nf-test (subworkflows/fastq_download_prefetch_fasterqdump_sratools, singularity)
1s
nf-core-lint (samtools/coverage)
1s
nf-test (subworkflows/fastq_align_star, conda)
1s
nf-core-lint (samtools/sort)
1s
nf-test (subworkflows/fastq_align_star, docker)
1s
nf-core-lint (samtools/convert)
1s
nf-test (subworkflows/fastq_align_star, singularity)
1s
nf-core-lint (samtools/sormadup)
1s
nf-test (subworkflows/fastq_align_dna, conda)
1s
nf-core-lint (svync)
1s
nf-test (subworkflows/fastq_align_dna, docker)
1s
nf-core-lint (multiqc)
1s
nf-test (subworkflows/fastq_align_dna, singularity)
1s
nf-core-lint (salmon/quant)
1s
nf-test (subworkflows/fastq_align_hisat2, conda)
1s
nf-core-lint (optitype)
1s
nf-test (subworkflows/fastq_align_hisat2, docker)
1s
nf-test (subworkflows/fastq_align_hisat2, singularity)
1s
nf-test (summarizedexperiment/summarizedexperiment, conda)
1s
nf-test (summarizedexperiment/summarizedexperiment, docker)
1s
nf-test (summarizedexperiment/summarizedexperiment, singularity)
1s
nf-test (gffread, conda)
1s
nf-test (gffread, docker)
1s
nf-test (gffread, singularity)
1s
nf-test (bedtools/genomecov, conda)
1s
nf-test (bedtools/genomecov, docker)
1s
nf-test (bedtools/genomecov, singularity)
1s
nf-test (custom/sratoolsncbisettings, conda)
1s
nf-test (custom/sratoolsncbisettings, docker)
1s
nf-test (custom/sratoolsncbisettings, singularity)
1s
nf-test (svanalyzer/svbenchmark, docker)
1s
nf-test (svanalyzer/svbenchmark, singularity)
1s
nf-test (bwa/mem, conda)
1s
nf-test (bwa/mem, docker)
1s
nf-test (bwa/mem, singularity)
1s
nf-test (mtmalign/align, conda)
1s
nf-test (mtmalign/align, docker)
1s
nf-test (mtmalign/align, singularity)
1s
nf-test (bbmap/bbsplit, conda)
1s
nf-test (bbmap/bbsplit, docker)
1s
nf-test (bbmap/bbsplit, singularity)
1s
nf-test (umicollapse, conda)
1s
nf-test (umicollapse, docker)
1s
nf-test (umicollapse, singularity)
1s
nf-test (kraken2/kraken2, conda)
1s
nf-test (kraken2/kraken2, docker)
1s
nf-test (kraken2/kraken2, singularity)
1s
nf-test (krakentools/extractkrakenreads, conda)
1s
nf-test (krakentools/extractkrakenreads, docker)
1s
nf-test (krakentools/extractkrakenreads, singularity)
1s
nf-test (resfinder/run, conda)
1s
nf-test (resfinder/run, docker)
1s
nf-test (resfinder/run, singularity)
1s
nf-test (seqtk/seq, conda)
1s
nf-test (seqtk/seq, docker)
1s
nf-test (seqtk/seq, singularity)
1s
nf-test (seqtk/sample, conda)
1s
nf-test (seqtk/sample, docker)
1s
nf-test (seqtk/sample, singularity)
1s
nf-test (seqtk/mergepe, conda)
1s
nf-test (seqtk/mergepe, docker)
1s
nf-test (seqtk/mergepe, singularity)
1s
nf-test (seqtk/cutn, conda)
1s
nf-test (seqtk/cutn, docker)
1s
nf-test (seqtk/cutn, singularity)
1s
nf-test (seqtk/subseq, conda)
1s
nf-test (seqtk/subseq, docker)
1s
nf-test (seqtk/subseq, singularity)
1s
nf-test (seqtk/rename, conda)
1s
nf-test (seqtk/rename, docker)
1s
nf-test (seqtk/rename, singularity)
1s
nf-test (geofetch, conda)
1s
nf-test (geofetch, docker)
1s
nf-test (geofetch, singularity)
1s
nf-test (happy/prepy, conda)
1s
nf-test (happy/prepy, docker)
1s
nf-test (happy/prepy, singularity)
1s
nf-test (cutadapt, conda)
1s
nf-test (cutadapt, docker)
1s
nf-test (cutadapt, singularity)
1s
nf-test (kallistobustools/count, conda)
1s
nf-test (kallistobustools/count, docker)
1s
nf-test (kallistobustools/count, singularity)
1s
nf-test (kallistobustools/ref, conda)
1s
nf-test (kallistobustools/ref, docker)
1s
nf-test (kallistobustools/ref, singularity)
1s
nf-test (picard/crosscheckfingerprints, conda)
1s
nf-test (picard/crosscheckfingerprints, docker)
1s
nf-test (picard/crosscheckfingerprints, singularity)
1s
nf-test (mmseqs/createtsv, conda)
1s
nf-test (mmseqs/createtsv, docker)
1s
nf-test (mmseqs/createtsv, singularity)
1s
nf-test (minimap2/align, conda)
1s
nf-test (minimap2/align, docker)
1s
nf-test (minimap2/align, singularity)
1s
nf-test (tcoffee/align, conda)
1s
nf-test (tcoffee/align, docker)
1s
nf-test (tcoffee/align, singularity)
1s
nf-test (ribotish/quality, conda)
1s
nf-test (ribotish/quality, docker)
1s
nf-test (ribotish/quality, singularity)
1s
nf-test (ribotish/predict, conda)
1s
nf-test (ribotish/predict, docker)
1s
nf-test (ribotish/predict, singularity)
1s
nf-test (umitools/dedup, conda)
1s
nf-test (umitools/dedup, docker)
1s
nf-test (umitools/dedup, singularity)
1s
nf-test (umitools/prepareforrsem, conda)
1s
nf-test (umitools/prepareforrsem, docker)
1s
nf-test (umitools/prepareforrsem, singularity)
1s
nf-test (umitools/extract, conda)
1s
nf-test (umitools/extract, docker)
1s
nf-test (umitools/extract, singularity)
1s
nf-test (tximeta/tximport, conda)
1s
nf-test (tximeta/tximport, docker)
1s
nf-test (tximeta/tximport, singularity)
1s
nf-test (preseq/lcextrap, conda)
1s
nf-test (preseq/lcextrap, docker)
1s
nf-test (preseq/lcextrap, singularity)
1s
nf-test (sratools/fasterqdump, conda)
1s
nf-test (sratools/fasterqdump, docker)
1s
nf-test (sratools/fasterqdump, singularity)
1s
nf-test (sratools/prefetch, conda)
1s
nf-test (sratools/prefetch, docker)
1s
nf-test (sratools/prefetch, singularity)
1s
nf-test (cellranger/count, docker)
1s
nf-test (cellranger/count, singularity)
1s
nf-test (untar, conda)
1s
nf-test (untar, docker)
1s
nf-test (untar, singularity)
1s
nf-test (trust4, conda)
1s
nf-test (trust4, docker)
1s
nf-test (trust4, singularity)
1s
nf-test (glimpse2/phase, conda)
1s
nf-test (glimpse2/phase, docker)
1s
nf-test (glimpse2/phase, singularity)
1s
nf-test (glimpse2/chunk, conda)
1s
nf-test (glimpse2/chunk, docker)
1s
nf-test (glimpse2/chunk, singularity)
1s
nf-test (glimpse2/splitreference, conda)
1s
nf-test (glimpse2/splitreference, docker)
1s
nf-test (glimpse2/splitreference, singularity)
1s
nf-test (gatk4/genomicsdbimport, conda)
1s
nf-test (gatk4/genomicsdbimport, docker)
1s
nf-test (gatk4/genomicsdbimport, singularity)
1s
nf-test (stringtie/stringtie, conda)
1s
nf-test (stringtie/stringtie, docker)
1s
nf-test (stringtie/stringtie, singularity)
1s
nf-test (tabix/bgzip, conda)
1s
nf-test (tabix/bgzip, docker)
1s
nf-test (tabix/bgzip, singularity)
1s
nf-test (tabix/tabix, conda)
1s
nf-test (tabix/tabix, docker)
1s
nf-test (tabix/tabix, singularity)
1s
nf-test (tabix/bgziptabix, conda)
1s
nf-test (tabix/bgziptabix, docker)
1s
nf-test (tabix/bgziptabix, singularity)
1s
nf-test (trimgalore, conda)
1s
nf-test (trimgalore, docker)
1s
nf-test (trimgalore, singularity)
1s
nf-test (ribotricer/prepareorfs, conda)
1s
nf-test (ribotricer/prepareorfs, docker)
1s
nf-test (ribotricer/prepareorfs, singularity)
1s
nf-test (ribotricer/detectorfs, conda)
1s
nf-test (ribotricer/detectorfs, docker)
1s
nf-test (ribotricer/detectorfs, singularity)
1s
nf-test (dupradar, conda)
1s
nf-test (dupradar, docker)
1s
nf-test (dupradar, singularity)
1s
nf-test (bakta/bakta, docker)
1s
nf-test (bakta/bakta, singularity)
1s
nf-test (samtools/coverage, conda)
1s
nf-test (samtools/coverage, docker)
1s
nf-test (samtools/coverage, singularity)
1s
nf-test (samtools/sort, conda)
1s
nf-test (samtools/sort, docker)
1s
nf-test (samtools/sort, singularity)
1s
nf-test (samtools/convert, conda)
1s
nf-test (samtools/convert, docker)
1s
nf-test (samtools/convert, singularity)
1s
nf-test (samtools/sormadup, conda)
1s
nf-test (samtools/sormadup, docker)
1s
nf-test (samtools/sormadup, singularity)
1s
nf-test (svync, conda)
1s
nf-test (svync, docker)
1s
nf-test (svync, singularity)
1s
nf-test (multiqc, conda)
1s
nf-test (multiqc, docker)
1s
nf-test (multiqc, singularity)
1s
nf-test (salmon/quant, conda)
1s
nf-test (salmon/quant, docker)
1s
nf-test (salmon/quant, singularity)
1s
nf-test (optitype, conda)
1s
nf-test (optitype, docker)
1s
nf-test (optitype, singularity)
1s
confirm-pass
1s
6m 51s