Introduction

sanger-tol/ear is a bioinformatics pipeline that generates the data files required for the the generation of ERGA Assembly Reports. Sanger-tol/ear nests two other sanger-tol pipelines (blobtoolkit and curationpretext).

1. Read the input yaml file (YAML_INPUT)
2. Run GFASTATS (GFASTARS)
3. Run MERQURYFK_MERQURYFK (MERQURYFK)
4. Run MAIN_MAPPING, longread single-end/paired-end mapping
5. Run GENERATE_SAMPLESHEET, generate a csv file required for SANGER_TOL_BTK.
6. Run SANGER_TOL_BTK, also known as SANGER-TOL/BLOBTOOLKIT a subpipline for SANGER-TOL/EAR
7. Run SANGER_TOL_CPRETEXT, also known as SANGER-TOL/CURATIONPRETEXT a subpipeline for SANGER-TOL/EAR.

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

The sanger-tol/ear pipeline requires a number of databases in place in order to run the blobtoolkit pipeline. These include:

• A blast nt database
• A Diamond blast uniprot database
• A Diamond blast nr database
• An NCBI taxdump
• An NCBI rankedlineage.dmp

Next, a yaml file containing the following should then be completed:

# General Vales for all subpiplines and modules
assembly_id: <NAME OF ASSEMBLY>
reference_hap1: <LOCATION OF PRIMARY ASSEMBLY FILE .FA>
reference_hap2: <LOCATION OF HAPLOTYPE ASSEBMLY FILE .FA>
reference_haplotigs: <LOCATION OF THE HAPLOTIGS FILE, REMOVED DURING CURATION .FA>

# If a mapped bam already exists use the below + --mapped TRUE on the nextflow command else ignore it and the pipeline will create it.
mapped_bam: <MAPPED BAM .BAM>

merquryfk:
  fastk_hist: <THE PATH TO THE .HIST FILE>
  fastk_ktab: <PATH TO THE DIRECTORY CONTAINING THE KTAB FILES, ENSURE THE HIDDEN FILES ARE HERE TOO>

# Used by both subpipelines
longread:
  type: <hifi|clr|ont|illumina>
  dir: <DIRECTORY OF LONGREAD FILES .FASTA.GZ>
curationpretext:
  aligner: <minimap2|BWAMEM>
  telomere_motif: <TELOMERE MOTIF OF SAMPLE>
  hic_dir: <DIRECTORY OF HIC READ FILES .CRAM AND .CRAI>
btk:
  taxid: 1464561
  lineages: < CSV LIST OF DATABASES TO USE: "insecta_odb10,diptera_odb10">
  gca_accession: GCA_0001 <DEFAULT, DO NOT CHANGE UNLESS YOU HAVE A GCA_ACCESSION FOR YOUR SPECIES >

  nt_database: <DIRECTORY CONTAINING BLAST DB>
  nt_database_prefix: <BLASTDB PREFIX>
  diamond_uniprot_database_path: <PATH TO reference_proteomes.dmnd FROM UNIPROT>
  diamond_nr_database_path: <PATH TO nr.dmnd>
  ncbi_taxonomy_path: <DIRECTORY CONTAINING THE TAXDUMP>
  ncbi_rankedlineage_path: <FOLDER CONTAINING THE rankedlineage.dmp FILE>
  config: <PATH TO ear/conf/sanger-tol-btk.config TO OVERWRITE PROCESS LIMITS>

Now, you can run the pipeline using:

nextflow run sanger-tol/ear -profile <singularity,docker> \\
   --input assets/idCulLati1.yaml \\
   --mapped TRUE \\ # OPTIONAL
   --steps ["", "btk", "cpretext", "merquryfk"] # OPTIONAL CSV LIST OF STEPS TO EXCLUDE FROM EXECUTION
   --outdir test

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

sanger-tol/ear was originally written by DLBPointon.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.