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

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/stats and 3 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 STITCH software. Variants location to impute are obtain through the legend file given

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

Samtools markduplicate SAM/BAM/CRAM file

markdupbamsamcram
Includes: samtools/collatesamtools/fixmatesamtools/sort and 1 more module

Performs methylation quantification based on negative readout of C to T conversion of 3-letter genome alignments using Methyldackel.

3-letter genomemethylation5mCmethylseqbisulphitebisulfitebam
Includes: methyldackel/extractmethyldackel/mbias