Builds the curated assembly FASTA from the most recent PretextView AGP file and, if a .bed decontamination file is set, removes remaining contamination intervals and regenerates the pretext map.

Steps:

1. Finds the latest *.agp_1 file in the working directory.
2. Runs pretext-to-asm to produce the curated FASTA.
3. If a .bed decon file is present, runs remove_contamination_bed via LSF (bsub -K) for each haplotype (merged) or for the single primary FASTA.
   • For merged assemblies the hap2 decon file is derived by substituting hap1 → hap2 (with a fallback for partially phased naming).
4. Submits curationpretext.sh to regenerate the pretext map (hap1 only for merged assemblies).

Copies curated assembly files and the pretext map into the curated directory for downstream QC.

For merged assemblies, empty placeholder files are also created for the haplotig FASTA and hap2 chromosome list to satisfy pipeline expectations. The most recently modified *normal.pretext file from the curationpretext output directory is selected and renamed to the canonical curated path under pretext_dir.

Sets up a local workstation directory for manual curation.

Creates a subdirectory named after the ToL ID in the current directory, touches a notes file, and copies all matching pretext maps from the tol server via scp.

Initialises the HPC working directory and decompresses the assembly FASTA.

Creates working_dir on disk, then concatenates the appropriate decontaminated FASTA file(s) into original.fa:

• Haploid/primary+haplotigs: single decontaminated.fa.gz derived from the decon file path.
• Merged (hap1/hap2, maternal/paternal, or primary/haplotigs): both haplotype FASTA files are concatenated in order.

Raises if scaffolds.tpf already exists in the working directory (guards against accidentally overwriting an in-progress curation).