A subworkflow for filtering differential abundance results

differentialabundanceexpressioncount matrixfold-change
Includes: limma/differentialdeseq2/differentialpropr/propd and 2 more modules

Extract archive(s) from any format Currently supported format are .gz, .tar.gz, .zip

archivegziptarzip
Includes: gunzipuntarunzip

A subworkflow for calling CNVs using WisecondorX

cnvbambedcramplotsgenomics
Includes: wisecondorx/convertwisecondorx/predict

Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.

gatk4mutect2genomicsdbimportcreatesomaticpanelofnormalsvariant_callinggenomicsdb_workspacepanel_of_normals
Included in: createpanelrefs
Includes: gatk4/mutect2gatk4/genomicsdbimportgatk4/createsomaticpanelofnormals and 2 more modules

umicollapse, index BAM file and run samtools stats, flagstat and idxstats

umidedupindexbamsamcram
Included in: lncpiperiboseqrnaseq
Includes: umicollapsesamtools/indexsamtools/stats and 3 more modules

UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats

umidedupindexbamsamcram
Included in: lncpipenascentriboseq and 1 more pipeline
Includes: umitools/dedupsamtools/indexsamtools/view and 4 more modules

BAM deduplication with UMI processing for both genome and transcriptome alignments

deduplicationUMIBAMgenometranscriptomeumicollapseumitools
Included in: lncpiperiboseqrnaseq
Includes: umitools/prepareforrsemsamtools/sortbam_dedup_stats_samtools_umicollapse and 2 more modules

Calculate contamination of the X-chromosome with ANGSD

angsdbamcontaminationdocounts
Includes: angsd/docountsangsd/contamination

Subworkflow to impute BAM files using QUILT software. Variants location to impute are obtain through the tsv file given. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used.

BAMimputationquilt
Includes: gawkquilt/quiltbcftools/index and 1 more module

Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used.

bamcramimputationquiltquilt2vcf
Includes: quilt/quilt2glimpse2/ligatebcftools/index

Subworkflow to impute BAM files using STITCH software. Variants location to impute are obtain through the legend file given. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used.

BAMimputationstitch
Includes: stitchbcftools/indexglimpse2/ligate

Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats

markduplicatesbamsamcram
Included in: atacseqchipseqcircdna and 4 more pipelines
Includes: picard/markduplicatessamtools/indexsamtools/stats and 3 more modules