Available Modules
Modules are reusable process definitions for Nextflow DSL2 pipelines. These modules are maintained in the sanger-tol/nf-core-modules repository. For guidance on writing modules, see the nf-core documentation.
Extracts ancestrally linked busco genes from a busco full table file.
Scripts to extract ancestrally linked busco genes.
1 pipelines
A tool to collect ODB lineages using the GOAT API (with the ENA API as a fallback).
Generate a CSV containing relevant ODB's to run for a given assembly.
1 pipelines
A tool to produce contig- and scaffold-level assembly statistics, including composition, length, N50 and L50 metrics.
1 pipelines
A tool to filter an assembly fasta based on FCSGX and TIARA summary files. This also generates a join FCSGX/TIARA summary file.
Filter an assembly with FCSGX and TIARA summary files.
0 pipelines
A script to determine whether contamination levels exceed given thresholds for an assembly.
Determine whether contamination levels exceed given thresholds for an assembly.
0 pipelines
A tool to filter FASTA headers and filter sequences by length.
Filter FASTA sequences by length to remove sequences below a specified threshold.
0 pipelines
Create a set of BED files, each describing a chunk of a FASTA
GNU awk
1 pipelines
Streams a BAM file into bedtools bamToBed with samtools (with optional filtering), then sorts the resulting BED file using GNU sort.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
BEDTools is an extensive suite of utilities for comparing genomic features in BED format.
1 pipelines
bgzip a sorted tab-delimited genome file and then create tabix indexes in TBI and CSI format when the coordinate / sequence length is within the supported range of each index format. Compressed files are accepted and will be decompressed on the fly.
Bgzip compresses or decompresses files in a similar manner to, and compatible with, gzip.
Generic indexer for TAB-delimited genome position files.
3 pipelines
Queries a BLAST DNA database from a FASTA/FASTQ/BAM/CRAM file containing query sequences.
BLAST finds regions of similarity between biological sequences.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
0 pipelines
Generate a samplesheet csv for sanger-tol/blobtoolkit
1 pipelines
Generate a params file in json format for sanger-tol/blobtoolkit
0 pipelines
Benchmarking Universal Single Copy Orthologs
BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
1 pipelines
Parse BUSCO genome-mode full_table.tsv and write three prefixed bedGraph files (Complete, Duplicated, Fragmented), sorted by sequence and numeric start; score is 100.
Convert BUSCO full_table.tsv genomic coordinates into sorted per-status bedGraph files.
Output filenames use task.ext.prefix (default meta.id), e.g. sample.complete_buscos.bedgraph.
0 pipelines
Converts BED file to contacts BED format using shell utilities.
GNU coreutils provides standard utilities such as paste and tr used during conversion.
0 pipelines
Aligns a subset of Hi-C reads from a CRAM file to a reference genome using bwa-mem2, pipes the resulting alignments through samtools fixmate and samtools sort, outputting an alignment in BAM format.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
2 pipelines
Determine the chunks to split a CRAM file into for alignment
not a real tool!
2 pipelines
Aligns a subset of sequencing reads from a CRAM file to a reference genome using minimap2, pipes the resulting alignments through samtools view (optional) and samtools sort, outputting an alignment in BAM format.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
0 pipelines
Aligns a subset of Hi-C reads from a CRAM file to a reference genome using minimap2, pipes the resulting alignments through filterfiveend.pl (included), samtools fixmate and samtools sort, outputting an alignment in BAM format.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
Filter alignments
2 pipelines
Generate a params file in json format for sanger-tol/curationpretext
0 pipelines
Aligns a subset of sequencing reads from a FASTx file to a reference genome using minimap2. Can either output the alignment in PAF format, or alternatively will pipe the resulting alignments through samtools view and samtools sort, outputting an alignment in BAM format.
The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
A versatile pairwise aligner for genomic and spliced nucleotide sequences.
3 pipelines
Index a FASTx file using pyfastx to enable random access to a slice of reads in the file. Also returns the raw count of reads in the file.
The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number.
3 pipelines
Parses FCS-GX (Fungal Contamination Screening - GX) result files and augments them with NCBI taxonomy lineage information to produce a comprehensive CSV output containing contamination screening results with taxonomic classification.
Parse FCS-GX result files and augment with NCBI taxonomy lineage information
0 pipelines
Runs FCS-GX (Foreign Contamination Screen - Genome eXtractor) to screen and remove foreign contamination from genome assemblies
The NCBI Foreign Contamination Screen. Genomic cross-species aligner, for contamination detection.
0 pipelines
A module for concatenation of gzipped or uncompressed files getting around UNIX terminal argument size
GNU find searches the directory tree rooted at each given starting-point by evaluating the given expression
pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
0 pipelines
Re-organise a fasta index into a preffered GenomeNote order
0 pipelines
Whole-genome assembly using PacBio HiFi reads. This module is a modified version of the original nf-core version: https://github.com/nf-core/modules/blob/master/modules/nf-core/hifiasm/main.nf
1 pipelines
Annotate aligned Long-C monomer BAM records: group alignments by concatemer read, order monomers, and assign fragment tags (FI, FD, BX) for downstream pairtools parsing.
Group alignments by read ID, filter by MAPQ, order monomers, and write FI/FD/BX BAM tags.
0 pipelines
Digest concatemer reads into monomers at restriction enzyme recognition sites.
Reads FASTQ/FASTA (optionally gzipped), BAM, or CRAM and writes gzipped FASTQ
monomers ready for alignment. BAM/CRAM are converted with samtools fastq
(reference FASTA required for CRAM). Optional digest_reads.py arguments such as
--min-len can be passed via task.ext.args.
Split concatemer read sequences at restriction enzyme cut sites and emit monomer reads as FASTQ.
Convert BAM/CRAM alignments to FASTQ before digestion
Python runtime for digest_reads.py
0 pipelines
Convert annotated Long-C monomer BAM alignments to .pairs.gz using pairtools parse2,
streaming output through bgzip.
CLI tools to process mapped Hi-C and chromatin conformation data; parse2 reports ligation junctions from complex walks in annotated alignments.
0 pipelines
Performs alignment of Illumina 10X sequencing data to a Longranger indexed reference genome.
Does not have a container configured - a pipeline using this module must supply one via the config file. The container defined in the module test is accessible interally to Sanger users only and will need to be changed if outside users wish to test the module.
Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.
1 pipelines
Creates indices of a fasta file required for alignment step
Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.
1 pipelines
Find all soft-masked regions in a Fasta file and print their coordinates in BED format
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files.
0 pipelines
Remove all soft-masking from a Fasta file by turning all lower-case sequence characters to upper case.
GNU awk
0 pipelines
Remap Hi-C alignments onto a curated AGP with juicer pre, sort pairs, and filter
invalid coordinates — equivalent to the zippypretext juicerc.sh wrapper.
Remap Hi-C contacts from a .bin or BAM onto scaffold coordinates in an AGP
using a contig-level FASTA index (juicer pre -q 0).
0 pipelines
Build a gzipped Juicer .pairs file from a sorted alignment table and juicerc
log — combining the zippypretext make_header.sh and makepairs.sh steps.
0 pipelines
Convert a PretextView-curated AGP file and input assembly FASTA into a corrected AGP
using agp-tpf-utils pretext-to-asm.
Utilities for Tree of Life AGP and TPF assembly files. This module runs
pretext-to-asm to remap a PretextView AGP onto the input assembly.
Output filename uses task.ext.prefix (default meta.id), e.g.
sample_corrected.hap1.1.primary.curated.agp when haplotype tags are present.
0 pipelines
Create a directory with clean BUSCO outputs
GNU coreutils provides standard utilities such as paste and tr used during conversion.
GNU tape archive program
2 pipelines
Merge multiple fixmated, sorted SAM/BAM/CRAM and then mark duplicates
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
3 pipelines
Run the core steps of the sanger-tol/telomere toolkit.
Scan the assembly for a telomeric repeat motif (default TTAGGG) on both strands.
Slide windows along scaffolds and flag regions where telomeric hits exceed a density threshold.
0 pipelines
Wrapper around the YaHS juicer_pre tool to create a valid sorted pairs file describing Hi-C contacts among scaffolds using contacts among contigs and the YaHS AGP file describing the makeup of scaffolds from those contigs.
YaHS, yet another Hi-C scaffolding tool.
1 pipelines