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A subworkflow for filtering differential abundance results

Included in: differentialabundance
Includes: limma/differentialdeseq2/differentialpropr/propd and 2 more modules

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

Includes: gunzipuntarunzip

Apply Base Quality Score Recalibration (BQSR) to a BAM or CRAM file using GATK4 ApplyBQSR. Supports scatter-gather across genomic intervals: when more than one interval file is supplied per sample, the interval-level outputs are merged back together with samtools merge. When no intervals are supplied (num_intervals: 0), ApplyBQSR is run once on the whole input and no merge step is performed.

Includes: gatk4/applybqsrsamtools/merge

A subworkflow for calling CNVs using WisecondorX

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.

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

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

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

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

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

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

Calculate contamination of the X-chromosome with ANGSD

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.

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.

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.

Includes: stitchbcftools/indexglimpse2/ligate