Fixed sort_bam description in meta.yml (#5462) #2

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Job	Run time
editorconfig	9s
prettier	49s
nf-test-changes	8s
pre-commit	1m 0s
pytest-changes	10s
pytest (ashlar, conda)	1s
pytest (ashlar, docker)	1s
pytest (ashlar, singularity)	1s
pytest (cellrangerarc/count, docker)	1s
pytest (cellrangerarc/count, singularity)	1s
pytest (gatk/unifiedgenotyper, conda)	1s
pytest (gatk/unifiedgenotyper, docker)	1s
pytest (gatk/unifiedgenotyper, singularity)	1s
pytest (gatk4/bedtointervallist, conda)	1s
pytest (gatk4/bedtointervallist, docker)	1s
pytest (gatk4/bedtointervallist, singularity)	1s
pytest (gatk4/cnnscorevariants, docker)	1s
pytest (gatk4/cnnscorevariants, singularity)	1s
pytest (gatk4/determinegermlinecontigploidy, docker)	1s
pytest (gatk4/germlinecnvcaller, docker)	1s
pytest (gatk4/germlinecnvcaller, singularity)	1s
pytest (gatk4/postprocessgermlinecnvcalls, docker)	1s
pytest (gatk4/postprocessgermlinecnvcalls, singularity)	1s
pytest (proteus/readproteingroups, conda)	1s
pytest (proteus/readproteingroups, docker)	1s
pytest (proteus/readproteingroups, singularity)	1s
pytest (shapeit5/ligate, conda)	1s
pytest (shapeit5/ligate, docker)	1s
pytest (shapeit5/ligate, singularity)	1s
pytest (subworkflows/vcf_phase_shapeit5, conda)	1s
pytest (subworkflows/vcf_phase_shapeit5, docker)	1s
pytest (subworkflows/vcf_phase_shapeit5, singularity)	1s
nf-core-lint (ashlar)	1s
nf-core-lint (cellrangerarc/count)	1s
nf-core-lint (gatk/unifiedgenotyper)	1s
nf-core-lint (gatk4/bedtointervallist)	1s
nf-core-lint (gatk4/cnnscorevariants)	1s
nf-core-lint (gatk4/determinegermlinecontigploidy)	1s
nf-core-lint (gatk4/germlinecnvcaller)	1s
nf-core-lint (gatk4/postprocessgermlinecnvcalls)	1s
nf-core-lint (proteus/readproteingroups)	1s
nf-core-lint (shapeit5/ligate)	1s
nf-core-lint (subworkflows/vcf_phase_shapeit5)	1s
nf-core-lint (rgi/cardannotation)	1s
nf-core-lint (rgi/main)	1s
nf-core-lint (umitools/extract)	1s
nf-core-lint (umitools/dedup)	1s
nf-core-lint (umitools/prepareforrsem)	1s
nf-core-lint (spaceranger/mkgtf)	1s
nf-core-lint (spaceranger/count)	1s
nf-core-lint (spaceranger/mkref)	1s
nf-core-lint (deepcell/mesmer)	1s
nf-core-lint (gffread)	1s
nf-core-lint (strelka/somatic)	1s
nf-core-lint (strelka/germline)	1s
nf-core-lint (tabix/tabix)	1s
nf-core-lint (tabix/bgziptabix)	1s
nf-core-lint (tabix/bgzip)	1s
nf-core-lint (htseq/count)	1s
nf-core-lint (anota2seq/anota2seqrun)	1s
nf-core-lint (tcoffee/tcs)	1s
nf-core-lint (tcoffee/align)	1s
nf-core-lint (fastqc)	1s
nf-core-lint (pyrodigal)	1s
nf-core-lint (krakentools/extractkrakenreads)	1s
nf-core-lint (gecco/run)	1s
nf-core-lint (deepvariant)	1s
nf-core-lint (svanalyzer/svbenchmark)	1s
nf-core-lint (ngsbits/samplegender)	1s
nf-core-lint (gtdbtk/classifywf)	1s
nf-core-lint (gatk4/splitncigarreads)	1s
nf-core-lint (gatk4/addorreplacereadgroups)	1s
nf-core-lint (gatk4/estimatelibrarycomplexity)	1s
nf-core-lint (gatk4/svannotate)	1s
nf-core-lint (gatk4/combinegvcfs)	1s
nf-core-lint (gatk4/svcluster)	1s
nf-core-lint (gatk4/bedtointervallist)	1s
nf-core-lint (gatk4/mutect2)	1s
nf-core-lint (lofreq/viterbi)	1s
nf-core-lint (vcftools)	1s
nf-core-lint (nanofilt)	1s
nf-core-lint (ensemblvep/vep)	1s
nf-core-lint (ensemblvep/download)	1s
nf-core-lint (phispy)	1s
nf-core-lint (cobrameta)	1s
nf-core-lint (taxonkit/name2taxid)	1s
nf-core-lint (seqtk/sample)	1s
nf-core-lint (seqtk/rename)	1s
nf-core-lint (seqtk/subseq)	1s
nf-core-lint (seqtk/cutn)	1s
nf-core-lint (seqtk/seq)	1s
nf-core-lint (seqtk/mergepe)	1s
nf-core-lint (seqfu/stats)	1s
nf-core-lint (bamclipper)	1s
nf-core-lint (geofetch)	1s
nf-core-lint (circularmapper/circulargenerator)	1s
nf-core-lint (trust4)	1s
nf-core-lint (happy/prepy)	1s
nf-core-lint (isoseq3/tag)	1s
nf-core-lint (tiddit/sv)	1s
nf-core-lint (dupradar)	1s
nf-core-lint (gawk)	1s
nf-core-lint (fastme)	1s
nf-core-lint (leviosam2/index)	1s
nf-core-lint (leviosam2/lift)	1s
nf-core-lint (celesta)	1s
nf-core-lint (kalign/align)	1s
nf-core-lint (merfin/hist)	1s
nf-core-lint (bbmap/bbsplit)	1s
nf-core-lint (bbmap/bbmerge)	1s
nf-core-lint (mosdepth)	1s
nf-core-lint (toulligqc)	1s
nf-core-lint (wisecondorx/convert)	1s
nf-core-lint (wisecondorx/gender)	1s
nf-core-lint (wisecondorx/predict)	1s
nf-core-lint (wisecondorx/newref)	1s
nf-core-lint (mygene)	1s
nf-core-lint (preseq/lcextrap)	1s
nf-core-lint (bases2fastq)	1s
nf-core-lint (sratools/prefetch)	1s
nf-core-lint (wittyer)	1s
nf-core-lint (bamcmp)	1s
nf-core-lint (dragmap/hashtable)	1s
nf-core-lint (dragmap/align)	1s
nf-core-lint (snpeff/snpeff)	1s
nf-core-lint (popscle/dscpileup)	1s
nf-core-lint (umicollapse)	1s
nf-core-lint (bedtools/genomecov)	1s
nf-core-lint (bedtools/sort)	1s
nf-core-lint (bedtools/merge)	1s
nf-core-lint (atlasgeneannotationmanipulation/gtf2featureannotation)	1s
nf-core-lint (stringtie/stringtie)	1s
nf-core-lint (fastx/collapser)	1s
nf-core-lint (decoupler/decoupler)	1s
nf-core-lint (glimpse/sample)	1s
nf-core-lint (glimpse/chunk)	1s
nf-core-lint (glimpse/concordance)	1s
nf-core-lint (glimpse/ligate)	1s
nf-core-lint (glimpse/phase)	1s
nf-core-lint (optitype)	1s
nf-core-lint (minimap2/align)	1s
nf-core-lint (minimap2/index)	1s
nf-core-lint (fastp)	1s
nf-core-lint (hmmer/hmmsearch)	1s
nf-core-lint (kallistobustools/count)	1s
nf-core-lint (kallistobustools/ref)	1s
nf-core-lint (cnvkit/batch)	1s
nf-core-lint (learnmsa/align)	1s
nf-core-lint (cutadapt)	1s
nf-core-lint (genomescope2)	1s
nf-core-lint (kraken2/kraken2)	1s
nf-core-lint (kraken2/build)	1s
nf-core-lint (kraken2/add)	1s
nf-core-lint (ale)	1s
nf-core-lint (ribotish/quality)	1s
nf-core-lint (ribotish/predict)	1s
nf-core-lint (pretextmap)	1s
nf-core-lint (cellranger/mkgtf)	1s
nf-core-lint (cellranger/count)	1s
nf-core-lint (cellranger/multi)	1s
nf-core-lint (cellranger/vdj)	1s
nf-core-lint (cellranger/mkref)	1s
nf-core-lint (cellranger/mkvdjref)	1s
nf-core-lint (amplify/predict)	1s
nf-core-lint (bakta/baktadbdownload)	1s
nf-core-lint (bakta/bakta)	1s
nf-core-lint (angsd/gl)	1s
nf-core-lint (iqtree)	1s
nf-core-lint (svync)	1s
nf-core-lint (quartonotebook)	1s
nf-core-lint (bcftools/stats)	1s
nf-core-lint (bcftools/sort)	1s
nf-core-lint (bcftools/filter)	1s
nf-core-lint (bowtie2/align)	1s
nf-core-lint (tximeta/tximport)	1s
nf-core-lint (controlfreec/assesssignificance)	1s
nf-core-lint (controlfreec/freec)	1s
nf-core-lint (controlfreec/freec2bed)	1s
nf-core-lint (controlfreec/makegraph2)	1s
nf-core-lint (controlfreec/freec2circos)	1s
nf-core-lint (controlfreec/makegraph)	1s
nf-core-lint (maltextract)	1s
nf-core-lint (openms/idmerger)	1s
nf-core-lint (openms/idfilter)	1s
nf-core-lint (openms/peptideindexer)	1s
nf-core-lint (openms/peakpickerhires)	1s
nf-core-lint (bwa/mem)	1s
nf-core-lint (mmseqs/createtsv)	1s
nf-core-lint (svtyper/svtypersso)	1s
nf-core-lint (prodigal)	1s
nf-core-lint (gtfsort)	1s
nf-core-lint (metamaps/mapdirectly)	1s
nf-core-lint (kaiju/mergeoutputs)	1s
nf-core-lint (igvreports)	1s
nf-core-lint (plink/hwe)	1s
nf-core-lint (plink/fastepistasis)	1s
nf-core-lint (plink/epistasis)	1s
nf-core-lint (plink/ld)	1s
nf-core-lint (plink/gwas)	1s
nf-core-lint (samtools/faidx)	1s
nf-core-lint (samtools/sort)	1s
nf-core-lint (samtools/convert)	1s
nf-core-lint (samtools/sormadup)	1s
nf-core-lint (summarizedexperiment/summarizedexperiment)	1s
nf-core-lint (scimap/spatiallda)	1s
nf-core-lint (crabz/compress)	1s
nf-core-lint (crabz/decompress)	1s
nf-core-lint (islandpath)	1s
nf-core-lint (gt/gff3validator)	1s
nf-core-lint (meryl/unionsum)	1s
nf-core-lint (meryl/count)	1s
nf-core-lint (meryl/histogram)	1s
nf-core-lint (trimgalore)	1s
nf-core-lint (cellpose)	1s
nf-core-lint (propr/propd)	1s
nf-core-lint (propr/propr)	1s
nf-core-lint (manta/somatic)	1s
nf-core-lint (manta/germline)	1s
nf-core-lint (manta/tumoronly)	1s
nf-core-lint (glimpse2/chunk)	1s
nf-core-lint (glimpse2/splitreference)	1s
nf-core-lint (glimpse2/ligate)	1s
nf-core-lint (glimpse2/phase)	1s
nf-core-lint (bamstats/generalstats)	1s
nf-core-lint (velocyto)	1s
nf-core-lint (bwamem2/index)	1s
nf-core-lint (bwamem2/mem)	1s
nf-core-lint (picard/addorreplacereadgroups)	1s
nf-core-lint (picard/markduplicates)	1s
nf-core-lint (picard/crosscheckfingerprints)	1s
nf-core-lint (ribotricer/detectorfs)	1s
nf-core-lint (ribotricer/prepareorfs)	1s
nf-core-lint (xengsort/index)	1s
nf-core-lint (molkartgarage/clahe)	1s
nf-core-lint (president)	1s
nf-core-lint (liftoff)	1s
nf-core-lint (subworkflows/quantify_pseudo_alignment)	1s
nf-core-lint (subworkflows/fastq_align_mapad)	1s
nf-core-lint (subworkflows/bam_markduplicates_picard)	1s
nf-core-lint (subworkflows/fastq_align_bowtie2)	1s
nf-core-lint (subworkflows/fastq_align_bwa)	1s
nf-core-lint (subworkflows/fastq_download_prefetch_fasterqdump_sratools)	1s
nf-core-lint (subworkflows/vcf_impute_glimpse)	1s
nf-core-lint (subworkflows/fastq_align_dna)	1s
nf-core-lint (subworkflows/fastq_taxonomic_profile_metaphlan)	1s
nf-core-lint (subworkflows/bam_sort_stats_samtools)	1s
nf-core-lint (subworkflows/fastq_fastqc_umitools_trimgalore)	1s
nf-core-lint (subworkflows/fastq_fastqc_umitools_fastp)	1s
nf-core-lint (subworkflows/fasta_build_add_kraken2)	1s
nf-core-lint (subworkflows/bam_create_som_pon_gatk)	1s
nf-core-lint (subworkflows/fastq_align_star)	1s
nf-core-lint (subworkflows/fastq_align_bamcmp_bwa)	1s
confirm-pass	1s
	6m 24s

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Fixed sort_bam description in meta.yml (#5462) #2

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Fixed sort_bam description in meta.yml (#5462) #2

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