nf-core/subworkflows
Browse the 124 subworkflows that are currently available as part of nf-core.
A subworkflow for filtering differential abundance results
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.
A subworkflow for calling CNVs using WisecondorX
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.
umicollapse, index BAM file and run samtools stats, flagstat and idxstats
UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats
BAM deduplication with UMI processing for both genome and transcriptome alignments
Calculate contamination of the X-chromosome with ANGSD
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.
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.
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.