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Subworkflows

Browse the 27 subworkflows from the sanger-tol/nf-core-modules repository.

Available Subworkflows

Subworkflows combine modules into reusable groups of processes for Nextflow DSL2 pipelines. These subworkflows are maintained in the sanger-tol/nf-core-modules repository. For guidance on writing subworkflows, see the nf-core documentation.

  • align 2
  • bam 2
  • ont 1
  • pacbio 1
  • longread 1
  • hic 1
  • plots 0
  • restructure 0
  • odbsearch 0
  • sanger-tol/busco 0
  • blobtk 0
  • merqury 0
  • blobtoolkit 0
  • adapter-trimming 0
  • trimming 0
  • adapters 0
  • bed 0
  • gap 0
  • bigwig 0
  • windowmaker 0
  • demultiplex 0
  • ancestral 0
  • duplicate-marking 0
  • masking 0
  • curation 0
  • juicer 0
  • regions 0
  • windows 0
  • statistics 0
  • markup 0
  • repeat 0
  • pairs 0
  • fastq 0
  • minimap2 0
  • pretext 0
  • telomere 0
  • classification 0
  • repeats 0
  • feature 0
  • chunk 0
  • csv 0
  • vcf 0
  • png 0
  • pdf 0
  • busco 0
  • merge 0
  • duplicate marking 0
  • cooler 0
  • contacts 0
  • mcool 0
  • bedgraph 0
  • qc 0
  • completeness 0
  • tabix 0
  • polishing 0
  • variant calling 0
  • scaffolding 0
  • fcsgx 0
  • purging 0
  • paf 0
  • linkage 0
  • mapping 0
  • duplication 0
  • coverage 0
  • haplotypes 0
  • bgzip 0
  • contact map 0
  • samtools 0
  • faidx 0
  • index 0
  • fasta 0
  • reference-based scaffolding 0
  • assembly 0
  • zippypretext 0

2 subworkflows; Clear filters

cram_map_illumina_hic

hic align bam

Maps Hi-C reads in unaligned CRAM format to a set of references.

8 components; 4 pipelines

cram_map_long_reads

longread pacbio ont align bam

Maps PacBio/ONT reads in unaligned CRAMs format to a set of references.

6 components; 1 pipelines

Decoding Earth's Diversity since 2019 Supported by
Wellcome Wellcome and Sanger Sanger
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