RepeatMasker_Nextflow.nf

Nextflow script for running RepeatMasker on large assemblies/chromosomes/contigs in a cluster environment.

Workflow Process:

• Breakup the input sequence into N-sized non-overlapping batches
• Search each batch using RepeatMasker with the provided options
• Adjust batch local output sequence names/coordinates to global sequence names/coordinates
• Combine files and fix linkage IDs in both out and align files (if alignments requested)
• Generate a summary file (similar to 'tbl' file)
• Compress output files

Prerequisites:

1. Java JDK 11-19
2. Nextflow 21 or 21
3. Three UCSC Utilities:
   • linux/windows: https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64
   • macos: https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64
     • twoBitToFa
     • faToTwoBit
     • bedSort
4. RepeatMasker 4.x installed and configured

Configuration:

• Edit the RepeatMasker_Nextflow.nf script and make the following customizations for your environment:
  • Set the dependency locations: "ucscToolsDir", and "repeatMaskerDir"
  • Optionally setup a cluster environment for your cluster (furher down in the script)

Parameters:

 --species         : Dfam species library ( or use inputLibrary for custom lib )
 --nolow           : Use RepeatMasker '-nolow' option.  Not recommended under normal
                     circumstances.  Gives a major boost to false positives.
 --xsmall          : Use RepeatMasker '-xsmall' option.
 --s               : Use RepeatMasker -s option -- not a big impact for RMBlast.
 --inputSequence   : FASTA file optionally compressed with gzip.
                 or 
 --inputSequenceDir: Directory containing many FASTA files optionally compressed with gzip.
 --inputLibrary    : Uncompressed FASTA file containing consensi.
 --outputDir       : Directory to store the results.  Should already exist.
 --engine          : Specify engine to use [ default: rmblast ]
 --batchSize       : Size of each cluster job in bp [ default: 50mb ]
 --cluster         : Either "local", "quanah", "nocona" or "griz"

Examples:

NOTE: On some clusters it will be necessary to use full paths to all files specified as parameters.

o Run with standard libraries and a specified species:

nextflow run /path/RepeatMasker_Nextflow.nf \
                --inputSequence /full_path_required/GCA_003113815.1.fna.gz \
                --species "human" \
                --cluster nocona

o Run with a custom library:

nextflow run /path/RepeatMasker_Nextflow.nf \
                --inputSequence /full_path_required/GCA_003113815.1.fna.gz \
                --inputLibrary /full_path_required/GCA_003113815.1-consensi.fa \
                --cluster griz

o Run more than one genome with the same parameters:

nextflow run /path/RepeatMasker_Nextflow.nf \
                --inputSequenceDir /full_path_required \
                --inputLibrary /full_path_required/GCA_003113815.1-consensi.fa \
                --cluster griz

Robert Hubley, 3/2020