Subworkflows » sanger-tol

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.

fasta_compress_index

fasta index faidx samtools bgzip

Compress and index a Fasta file in multiple formats

3 components; 0 pipelines

fasta_purge_retained_haplotype

fasta purging haplotypes coverage duplication

Purge retained haplotypic duplications from an assembly using purge_dups.

If alternate assembly or alternate assemblies are provided, these will all be concatenated with the purged haplotigs.

9 components; 1 pipelines

fastx_map_long_reads

fasta mapping chunk bam paf

Map reads from a FASTx file to a reference in chunks, outputting the alignments in BAM or PAF format. If BAM alignment is chosen, the output BAM files are merged.

4 components; 4 pipelines

fcsgx_parsecsv

fcsgx csv fasta classification

Run FCS_GX to classify sequences in an assembly, parse the output files into a single CSV.

3 components; 0 pipelines

gap_finder

gap bed adapters trimming fasta

Generate a bed file containing gaps and their length

3 components; 1 pipelines

read_coverage

mapping minimap2 coverage bedgraph fastq fasta

Map read inputs and emit alignment and coverage bedGraph outputs

4 components; 0 pipelines

soft_masked_fasta_repeats

fasta bed bgzip tabix

Extract the position of the repeats from a soft-masked Fasta file into a BED file, and compress and index it with tabix.

2 components; 0 pipelines

telo_finder

telomere windows regions fasta tabix

Run telomere/findtelomere on an assembly and motif string; optionally bgzip/tabix strand BED (*.fwd.telomere.bed, *.rev.telomere.bed) and windows files (*.windows or *.fwd.windows / *.rev.windows).

2 components; 1 pipelines