[BUG]: There is no command in phg prepare-slurm-align-file

[sidevshiy]

Description

Hello, I used preparation script from SLURM usage docs but it seems like there is no command "prepare-slurm-align-file".

Usage: phg [] []...

Options: --version Show the version and exit -h, --help Show this message and exit

Commands: setup-environment Create a conda environment for PHG initdb Create TileDB datasets for g.vcf and h.vcf files create-ranges Create a BED file of reference ranges from a GFF file prepare-assemblies Annotate FASTA file Id lines with sample names, write new FASTAs with name .fa agc-compress Create a single AGC compressed file from an input of FASTA files created with the phg prepare-assemblies command align-assemblies Align prepared assembly fasta files using AnchorWave. create-anchorwave-dotplot create a dot plot stored in PNG file from anchowave anchorspro file create-ref-vcf Create and load to tiledb a haplotype VCF for the reference genome create-maf-vcf Create g.vcf and h.vcf files from AnchorWave MAF files gvcf2hvcf Create h.vcf files from existing PHG created g.vcf files hvcf2gvcf Create g.vcf file for a PHG pathing h.vcf using data from existing PHG created g.vcf files load-vcf Load g.vcf and h.vcf files into TileDB datasets export-vcf Export given samples to an h.vcf file build-kmer-index Create a kmer index for a HaplotypeGraph. By default the file will be written to

/kmerIndex.txt map-kmers Map Kmers to the pangenome reference find-paths Impute best path(s) using read mappings. create-fasta-from-hvcf Create a FASTA file from a h.vcf file or TileDB directly merge-hvcfs Merge multiple HVCF files into a single HVCF file. merge-gvcfs Merge GVCF files into Single VCF file calc-vcf-metrics Calculate quality control metrics on g.vcf files start-server Starts PHGv2 BrAPI Server ### Expected behavior _No response_ ### PHG version phg version 2.3.7.144

[lynnjo]

ah - you're right! The code is there but not visible. We should have that fixed today - I'll post a message when a new version with this fix is available.

[lynnjo]

phg.tar file with Tag 2.3.8.145 and later has this fix. Let me know if you still see problems - thanks.

[sidevshiy]

Thank you!