sample,fastq_1,fastq_2
sample1,/path/to/fastq/files/sample1.R1.fastq.gz,/path/to/fastq/files/sample1.R2.fastq.gz
sample2,/path/to/fastq/files/sample2.R1.fastq.gz,/path/to/fastq/files/sample2.R2.fastq.gz

sample,results
sample1,expectedSpecies
sample2,expectedSpecies2

specimen_id name_last   name_first  birth_date  sex pt_city pt_state    pt_zip  pt_county   specimen_host   isolation_source    source_other    healthcare_origin   healthcare_state    healthcare_zip  submitter_name  submitter_state submitter_zip   organism_genus  organism_species    collect_date    date_received
sample1 person1 person1 9/19/1948   1   ATHENS  OH  45701   ATHENS  1   SWAB_WOUND      LAURELS OF ATHENS, THE  OH  45701   HEALTH_ASSOCIATES   OH  44132   ACINETOBACTER   BAUMANNII   8/6/2024    8/14/2024
sample2 person2 person2 4/26/1953   2   LEBANON IL  62254   ST. CLAIR   1   SWAB_WOUND          IL      HEALTH_ASSOCIATES   OH  44132   ACINETOBACTER   BAUMANNII   7/31/2024   8/14/2024
sample3 person3 person3 3/17/1957   1   BELLEVUE    OH  44811   SANDUSKY    1   URINE_CATHETER (STRAIGHT)       CLEVELAND CLINIC    OH  44195   HEALTH_ASSOCIATES   OH  44106   PSEUDOMONAS AERUGINOSA  8/11/2024   8/16/2024

#!/bin/bash
# bash reformat_kraken2.sh 202401 k2_standard_08gb_20240112.tar.gz

tag=$1
kraken_db=$2
kraken_output="k2_standard_08gb_reformat_${tag}.tar.gz"

if [[ ${kraken_db} == *.tar.gz ]]; then
        echo "Preparing K2 directory: from ${kraken_db} to  ${kraken_output}"

        # Use standard gzip for decompression
        tar -xzf "${kraken_db}" || {
                echo "Error: Failed to extract ${kraken_db}" >&2
                exit 1
        }

        # create the final dir
        mkdir -p "${kraken_output}"
        mv *.kmer_distrib *.k2d seqid2taxid.map inspect.txt ktaxonomy.tsv "${kraken_output}" 2>/dev/null || {
                echo "Warning: Some expected files were not found."
        }
elif
        echo "Output already exists: ${kraken_output}"
fi

- REFSEQ_20240124_Bacteria_complete.msh.gz
- mlst_db_20240124.tar.gz
- phiX.fasta
- nodes_20240129.dmp.gz
- names_20240129.dmp.gz
- HyperVirulence_20220414.fasta
- ResGANNCBI_20240131_srst2.fasta
- PF-Replicons_20240124.fasta
- amrfinderdb_v3.12_20240131.1.tar.gz
- NCBI_Assembly_stats_20240124.txt