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Added new module for Toulligqc (#5131) #3

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Added new module for Toulligqc (#5131)

Added new module for Toulligqc (#5131) #3

Run time

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Job Run time
editorconfig
9s
prettier
45s
nf-test-changes
4s
pre-commit
46s
pytest-changes
5s
nf-test (subworkflows/fastq_align_mapad, conda)
1s
nf-test (subworkflows/fastq_align_mapad, docker)
1s
nf-test (subworkflows/fastq_align_mapad, singularity)
1s
nf-test (subworkflows/bam_markduplicates_picard, conda)
1s
nf-test (subworkflows/bam_markduplicates_picard, docker)
1s
nf-test (subworkflows/bam_markduplicates_picard, singularity)
1s
nf-test (subworkflows/fastq_taxonomic_profile_metaphlan, conda)
1s
nf-test (subworkflows/fastq_taxonomic_profile_metaphlan, docker)
1s
nf-test (subworkflows/fastq_taxonomic_profile_metaphlan, singularity)
1s
nf-test (subworkflows/fastq_align_dna, conda)
1s
nf-test (subworkflows/fastq_align_dna, docker)
1s
nf-test (subworkflows/fastq_align_dna, singularity)
1s
nf-test (celesta, docker)
1s
nf-test (celesta, singularity)
1s
nf-test (dragmap/align, conda)
1s
nf-test (dragmap/align, docker)
1s
nf-test (dragmap/align, singularity)
1s
nf-test (kalign/align, conda)
1s
nf-test (kalign/align, docker)
1s
nf-test (kalign/align, singularity)
1s
nf-test (kaiju/mergeoutputs, conda)
1s
nf-test (kaiju/mergeoutputs, docker)
1s
nf-test (kaiju/mergeoutputs, singularity)
1s
nf-test (toulligqc, conda)
1s
nf-test (toulligqc, docker)
1s
nf-test (toulligqc, singularity)
1s
nf-test (circularmapper/circulargenerator, conda)
1s
nf-test (circularmapper/circulargenerator, docker)
1s
nf-test (circularmapper/circulargenerator, singularity)
1s
nf-test (wittyer, docker)
1s
nf-test (wittyer, singularity)
1s
nf-test (openms/peptideindexer, conda)
1s
nf-test (openms/peptideindexer, docker)
1s
nf-test (openms/peptideindexer, singularity)
1s
nf-test (openms/idmerger, conda)
1s
nf-test (openms/idmerger, docker)
1s
nf-test (openms/idmerger, singularity)
1s
nf-test (deepvariant, docker)
1s
nf-test (deepvariant, singularity)
1s
nf-test (kraken2/build, conda)
1s
nf-test (kraken2/build, docker)
1s
nf-test (kraken2/build, 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 (quartonotebook, docker)
1s
nf-test (quartonotebook, singularity)
1s
nf-test (president, conda)
1s
nf-test (president, docker)
1s
nf-test (president, singularity)
1s
nf-test (cnvkit/batch, conda)
1s
nf-test (cnvkit/batch, docker)
1s
nf-test (cnvkit/batch, singularity)
1s
nf-test (bamclipper, conda)
1s
nf-test (bamclipper, docker)
1s
nf-test (bamclipper, singularity)
1s
nf-test (decoupler/decoupler, conda)
1s
nf-test (decoupler/decoupler, docker)
1s
nf-test (decoupler/decoupler, singularity)
1s
nf-test (strelka/germline, conda)
1s
nf-test (strelka/germline, docker)
1s
nf-test (strelka/germline, singularity)
1s
nf-test (strelka/somatic, conda)
1s
nf-test (strelka/somatic, docker)
1s
nf-test (strelka/somatic, singularity)
1s
nf-test (isoseq3/tag, conda)
1s
nf-test (isoseq3/tag, docker)
1s
nf-test (isoseq3/tag, singularity)
1s
nf-test (plink/epistasis, conda)
1s
nf-test (plink/epistasis, docker)
1s
nf-test (plink/epistasis, singularity)
1s
nf-test (plink/ld, conda)
1s
pytest (ashlar, conda)
1s
nf-test (plink/ld, docker)
1s
pytest (ashlar, docker)
1s
nf-test (plink/ld, singularity)
1s
pytest (ashlar, singularity)
1s
nf-test (plink/fastepistasis, conda)
1s
pytest (gatk4/cnnscorevariants, docker)
1s
nf-test (plink/fastepistasis, docker)
1s
pytest (gatk4/cnnscorevariants, singularity)
1s
pytest (gatk4/determinegermlinecontigploidy, docker)
1s
nf-test (plink/fastepistasis, singularity)
1s
pytest (gatk4/germlinecnvcaller, docker)
1s
nf-test (plink/gwas, conda)
1s
pytest (gatk4/germlinecnvcaller, singularity)
1s
nf-test (plink/gwas, docker)
1s
pytest (gatk4/postprocessgermlinecnvcalls, docker)
1s
nf-test (plink/gwas, singularity)
1s
pytest (gatk4/postprocessgermlinecnvcalls, singularity)
1s
nf-test (meryl/count, conda)
1s
pytest (shapeit5/ligate, conda)
1s
nf-test (meryl/count, docker)
1s
nf-test (meryl/count, singularity)
1s
pytest (shapeit5/ligate, docker)
1s
nf-test (meryl/unionsum, conda)
1s
pytest (shapeit5/ligate, singularity)
1s
nf-test (meryl/unionsum, docker)
1s
pytest (subworkflows/vcf_phase_shapeit5, conda)
1s
nf-test (meryl/unionsum, singularity)
1s
pytest (subworkflows/vcf_phase_shapeit5, docker)
1s
nf-test (meryl/histogram, conda)
1s
pytest (subworkflows/vcf_phase_shapeit5, singularity)
1s
nf-test (meryl/histogram, docker)
1s
nf-test (meryl/histogram, singularity)
1s
nf-test (kallistobustools/count, conda)
1s
nf-test (kallistobustools/count, docker)
1s
nf-test (kallistobustools/count, singularity)
1s
nf-test (picard/addorreplacereadgroups, conda)
1s
nf-test (picard/addorreplacereadgroups, docker)
1s
nf-test (picard/addorreplacereadgroups, singularity)
1s
nf-test (picard/markduplicates, conda)
1s
nf-test (picard/markduplicates, docker)
1s
nf-test (picard/markduplicates, singularity)
1s
nf-test (bases2fastq, docker)
1s
nf-test (metamaps/mapdirectly, conda)
1s
nf-test (metamaps/mapdirectly, docker)
1s
nf-test (metamaps/mapdirectly, singularity)
1s
nf-test (ensemblvep/vep, docker)
1s
nf-test (ensemblvep/vep, singularity)
1s
nf-core-lint (ashlar)
1s
nf-test (ensemblvep/download, conda)
1s
nf-core-lint (gatk4/cnnscorevariants)
1s
nf-test (ensemblvep/download, docker)
1s
nf-core-lint (gatk4/determinegermlinecontigploidy)
1s
nf-test (ensemblvep/download, singularity)
1s
nf-core-lint (gatk4/germlinecnvcaller)
1s
nf-test (bwamem2/mem, conda)
1s
nf-core-lint (gatk4/postprocessgermlinecnvcalls)
1s
nf-test (bwamem2/mem, docker)
1s
nf-core-lint (shapeit5/ligate)
1s
nf-test (bwamem2/mem, singularity)
1s
nf-core-lint (subworkflows/vcf_phase_shapeit5)
1s
nf-test (tcoffee/tcs, conda)
1s
nf-core-lint (subworkflows/fastq_align_mapad)
1s
nf-test (tcoffee/tcs, docker)
1s
nf-core-lint (subworkflows/bam_markduplicates_picard)
1s
nf-test (tcoffee/tcs, singularity)
1s
nf-core-lint (subworkflows/fastq_taxonomic_profile_metaphlan)
1s
nf-test (tiddit/sv, conda)
1s
nf-core-lint (subworkflows/fastq_align_dna)
1s
nf-test (tiddit/sv, docker)
1s
nf-core-lint (celesta)
1s
nf-test (tiddit/sv, singularity)
1s
nf-core-lint (dragmap/align)
1s
nf-test (gecco/run, conda)
1s
nf-core-lint (kalign/align)
1s
nf-test (gecco/run, docker)
1s
nf-core-lint (kaiju/mergeoutputs)
1s
nf-test (gecco/run, singularity)
1s
nf-core-lint (toulligqc)
1s
nf-test (svtyper/svtypersso, conda)
1s
nf-core-lint (circularmapper/circulargenerator)
1s
nf-test (svtyper/svtypersso, docker)
1s
nf-core-lint (wittyer)
1s
nf-test (svtyper/svtypersso, singularity)
1s
nf-core-lint (openms/peptideindexer)
1s
nf-test (cellranger/vdj, docker)
1s
nf-core-lint (openms/idmerger)
1s
nf-test (cellranger/vdj, singularity)
1s
nf-core-lint (deepvariant)
1s
nf-test (cellranger/count, docker)
1s
nf-core-lint (kraken2/build)
1s
nf-test (cellranger/count, singularity)
1s
nf-core-lint (kraken2/kraken2)
1s
nf-test (cellranger/multi, docker)
1s
nf-core-lint (krakentools/extractkrakenreads)
1s
nf-test (cellranger/multi, singularity)
1s
nf-core-lint (quartonotebook)
1s
nf-test (cellranger/mkgtf, docker)
1s
nf-core-lint (president)
1s
nf-test (cellranger/mkgtf, singularity)
1s
nf-core-lint (cnvkit/batch)
1s
nf-test (cellranger/mkvdjref, docker)
1s
nf-core-lint (bamclipper)
1s
nf-test (cellranger/mkvdjref, singularity)
1s
nf-core-lint (decoupler/decoupler)
1s
nf-test (cellranger/mkref, docker)
1s
nf-core-lint (strelka/germline)
1s
nf-test (cellranger/mkref, singularity)
1s
nf-core-lint (strelka/somatic)
1s
nf-test (controlfreec/freec, conda)
1s
nf-core-lint (isoseq3/tag)
1s
nf-test (controlfreec/freec, docker)
1s
nf-core-lint (plink/epistasis)
1s
nf-test (controlfreec/freec, singularity)
1s
nf-test (controlfreec/makegraph, conda)
1s
nf-core-lint (plink/ld)
1s
nf-test (controlfreec/makegraph, docker)
1s
nf-core-lint (plink/fastepistasis)
1s
nf-test (controlfreec/makegraph, singularity)
1s
nf-core-lint (plink/gwas)
1s
nf-core-lint (meryl/count)
1s
nf-test (controlfreec/makegraph2, conda)
1s
nf-core-lint (meryl/unionsum)
1s
nf-test (controlfreec/makegraph2, docker)
1s
nf-core-lint (meryl/histogram)
1s
nf-test (controlfreec/makegraph2, singularity)
1s
nf-core-lint (kallistobustools/count)
1s
nf-test (controlfreec/assesssignificance, conda)
1s
nf-core-lint (picard/addorreplacereadgroups)
1s
nf-test (controlfreec/assesssignificance, docker)
1s
nf-core-lint (picard/markduplicates)
1s
nf-test (controlfreec/assesssignificance, singularity)
1s
nf-core-lint (bases2fastq)
1s
nf-test (rgi/cardannotation, conda)
1s
nf-core-lint (metamaps/mapdirectly)
1s
nf-test (rgi/cardannotation, docker)
1s
nf-core-lint (ensemblvep/vep)
1s
nf-test (rgi/cardannotation, singularity)
1s
nf-core-lint (ensemblvep/download)
1s
nf-test (rgi/main, conda)
1s
nf-core-lint (bwamem2/mem)
1s
nf-test (rgi/main, docker)
1s
nf-core-lint (tcoffee/tcs)
1s
nf-test (rgi/main, singularity)
1s
nf-core-lint (tiddit/sv)
1s
nf-test (gatk4/svannotate, conda)
1s
nf-core-lint (gecco/run)
1s
nf-test (gatk4/svannotate, docker)
1s
nf-test (gatk4/svannotate, singularity)
1s
nf-test (gatk4/estimatelibrarycomplexity, conda)
1s
nf-core-lint (svtyper/svtypersso)
1s
nf-test (gatk4/estimatelibrarycomplexity, docker)
1s
nf-test (gatk4/estimatelibrarycomplexity, singularity)
1s
nf-core-lint (cellranger/vdj)
1s
nf-test (gatk4/svcluster, conda)
1s
nf-core-lint (cellranger/count)
1s
nf-test (gatk4/svcluster, docker)
1s
nf-core-lint (cellranger/multi)
1s
nf-core-lint (cellranger/mkgtf)
1s
nf-test (gatk4/svcluster, singularity)
1s
nf-core-lint (cellranger/mkvdjref)
1s
nf-test (gatk4/combinegvcfs, conda)
1s
nf-core-lint (cellranger/mkref)
1s
nf-test (gatk4/combinegvcfs, docker)
1s
nf-core-lint (controlfreec/freec)
1s
nf-core-lint (controlfreec/makegraph)
1s
nf-test (gatk4/combinegvcfs, singularity)
1s
nf-core-lint (controlfreec/makegraph2)
1s
nf-test (gatk4/addorreplacereadgroups, conda)
1s
nf-test (gatk4/addorreplacereadgroups, docker)
1s
nf-core-lint (controlfreec/assesssignificance)
1s
nf-test (gatk4/addorreplacereadgroups, singularity)
1s
nf-core-lint (rgi/cardannotation)
1s
nf-test (mygene, conda)
1s
nf-core-lint (rgi/main)
1s
nf-core-lint (gatk4/svannotate)
1s
nf-test (mygene, docker)
1s
nf-core-lint (gatk4/estimatelibrarycomplexity)
1s
nf-test (mygene, singularity)
1s
nf-core-lint (gatk4/svcluster)
1s
nf-test (pretextmap, conda)
1s
nf-core-lint (gatk4/combinegvcfs)
1s
nf-test (pretextmap, docker)
1s
nf-core-lint (gatk4/addorreplacereadgroups)
1s
nf-test (pretextmap, singularity)
1s
nf-core-lint (mygene)
1s
nf-test (hmmer/hmmsearch, conda)
1s
nf-test (hmmer/hmmsearch, docker)
1s
nf-core-lint (pretextmap)
1s
nf-test (hmmer/hmmsearch, singularity)
1s
nf-core-lint (hmmer/hmmsearch)
1s
nf-test (taxonkit/name2taxid, conda)
1s
nf-core-lint (taxonkit/name2taxid)
1s
nf-test (taxonkit/name2taxid, docker)
1s
nf-test (taxonkit/name2taxid, singularity)
1s
nf-test (bamstats/generalstats, conda)
1s
nf-core-lint (bamstats/generalstats)
1s
nf-test (bamstats/generalstats, docker)
1s
nf-core-lint (scimap/spatiallda)
1s
nf-test (bamstats/generalstats, singularity)
1s
nf-core-lint (bakta/bakta)
1s
nf-test (scimap/spatiallda, docker)
1s
nf-core-lint (islandpath)
1s
nf-test (scimap/spatiallda, singularity)
1s
nf-core-lint (molkartgarage/clahe)
1s
nf-test (bakta/bakta, docker)
1s
nf-core-lint (crabz/compress)
1s
nf-test (bakta/bakta, singularity)
1s
nf-core-lint (crabz/decompress)
1s
nf-test (islandpath, docker)
1s
nf-test (islandpath, singularity)
1s
nf-core-lint (gtdbtk/classifywf)
1s
nf-test (molkartgarage/clahe, docker)
1s
nf-test (molkartgarage/clahe, singularity)
1s
nf-core-lint (popscle/dscpileup)
1s
nf-core-lint (igvreports)
1s
nf-test (crabz/compress, conda)
1s
nf-core-lint (manta/germline)
1s
nf-test (crabz/compress, docker)
1s
nf-core-lint (manta/somatic)
1s
nf-test (crabz/compress, singularity)
1s
nf-core-lint (manta/tumoronly)
1s
nf-test (crabz/decompress, conda)
1s
nf-core-lint (leviosam2/lift)
1s
nf-test (crabz/decompress, docker)
1s
nf-core-lint (leviosam2/index)
1s
nf-test (crabz/decompress, singularity)
1s
nf-core-lint (vcftools)
1s
nf-test (gtdbtk/classifywf, conda)
1s
nf-core-lint (genomescope2)
1s
nf-test (gtdbtk/classifywf, docker)
1s
nf-core-lint (learnmsa/align)
1s
nf-test (gtdbtk/classifywf, singularity)
1s
nf-core-lint (nanofilt)
1s
nf-test (popscle/dscpileup, conda)
1s
nf-core-lint (mosdepth)
1s
nf-test (popscle/dscpileup, docker)
1s
nf-core-lint (bcftools/stats)
1s
nf-test (popscle/dscpileup, singularity)
1s
nf-core-lint (bcftools/filter)
1s
nf-test (igvreports, conda)
1s
nf-test (igvreports, docker)
1s
nf-test (igvreports, singularity)
1s
nf-test (manta/germline, conda)
1s
nf-test (manta/germline, docker)
1s
nf-test (manta/germline, singularity)
1s
nf-test (manta/somatic, conda)
1s
nf-test (manta/somatic, docker)
1s
nf-test (manta/somatic, singularity)
1s
nf-test (manta/tumoronly, conda)
1s
nf-test (manta/tumoronly, docker)
1s
nf-test (manta/tumoronly, singularity)
1s
nf-test (leviosam2/lift, conda)
1s
nf-test (leviosam2/lift, docker)
1s
nf-test (leviosam2/lift, singularity)
1s
nf-test (leviosam2/index, conda)
1s
nf-test (leviosam2/index, docker)
1s
nf-test (leviosam2/index, singularity)
1s
nf-test (vcftools, conda)
1s
nf-test (vcftools, docker)
1s
nf-test (vcftools, singularity)
1s
nf-test (genomescope2, conda)
1s
nf-test (genomescope2, docker)
1s
nf-test (genomescope2, singularity)
1s
nf-test (learnmsa/align, conda)
1s
nf-test (learnmsa/align, docker)
1s
nf-test (learnmsa/align, singularity)
1s
nf-test (nanofilt, conda)
1s
nf-test (nanofilt, docker)
1s
nf-test (nanofilt, singularity)
1s
nf-test (mosdepth, conda)
1s
nf-test (mosdepth, docker)
1s
nf-test (mosdepth, singularity)
1s
nf-test (bcftools/stats, conda)
1s
nf-test (bcftools/stats, docker)
1s
nf-test (bcftools/stats, singularity)
1s
nf-test (bcftools/filter, conda)
1s
nf-test (bcftools/filter, docker)
1s
nf-test (bcftools/filter, singularity)
1s
confirm-pass
1s
7m 44s