diff --git a/.dockstore.yml b/.dockstore.yml
index 2e5185717..0c9012485 100644
--- a/.dockstore.yml
+++ b/.dockstore.yml
@@ -414,3 +414,13 @@ workflows:
     primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz_general.wdl
     testParameterFiles:
       - /empty.json
+  - name: blastoff
+    subclass: WDL
+    primaryDescriptorPath: /pipes/WDL/workflows/blastoff.wdl
+    testParameterFiles:
+      - /empty.json
+  - name: chunk_blast
+    subclass: WDL
+    primaryDescriptorPath: /pipes/WDL/workflows/megablast_chunk.wdl
+    testParameterFiles:
+      - /empty.json
diff --git a/pipes/WDL/tasks/tasks_megablast.wdl b/pipes/WDL/tasks/tasks_megablast.wdl
new file mode 100644
index 000000000..5e6fe67e2
--- /dev/null
+++ b/pipes/WDL/tasks/tasks_megablast.wdl
@@ -0,0 +1,390 @@
+version 1.0
+
+task trim_rmdup_subsamp {
+    meta {
+        description: "Trim reads via trimmomatic, remove duplicate reads, and subsample to a desired read count (default of 100,000), bam in, bam out. "
+    }
+    input { 
+        File inBam
+        String bam_basename = basename(inBam, '.bam')                 
+        File clipDb
+        Int n_reads=10000000
+        Int machine_mem_gb = 128
+        Int cpu = 16
+        Int disk_size_gb = 100 
+        String docker ="quay.io/broadinstitute/viral-assemble:2.3.1.3" #skip-global-version-pin
+    }
+    parameter_meta {
+        inBam: {
+            description: "Input BAM file",
+            category: "required"
+        }
+        clipDb: {
+            description: "FASTA file that has a list of sequences to trim from the end of reads. These includes various sequencing adapters and primer sequences that may be on the ends of reads, including those for most of the Illumina kits we use.",
+            category: "required"
+        }
+        n_reads: {
+            description: "Maximum number of reads set to 10000000 by default.",
+            category: "required"
+        }
+    }
+    command <<<
+        set -ex o pipefail
+        assembly.py --version | tee VERSION
+        #BAM ->FASTQ-> OutBam? https://github.com/broadinstitute/viral-assemble/blob/80bcc1da5c6a0174362ca9fd8bc0b49ee0b4103b/assembly.py#L91
+        assembly.py trim_rmdup_subsamp \
+        "~{inBam}" \
+        "~{clipDb}" \
+        "$(pwd)/outbam.bam" \
+        ~{'--n_reads=' + n_reads}
+
+
+        #samtools [OutBam -> FASTA]
+        #-f 4 (f = include only) (4 = unmapped reads) https://broadinstitute.github.io/picard/explain-flags.html
+        samtools fasta "$(pwd)/outbam.bam" > "~{bam_basename}.fasta"
+    >>>
+output {
+    File    trimmed_fasta = "~{bam_basename}.fasta"
+}
+runtime {
+    docker:docker
+    memory: machine_mem_gb + "GB"
+    cpu: cpu
+    disks: "local-disk " + disk_size_gb + " LOCAL"
+    dx_instance_type: "n2-highmem-4"
+}
+}
+
+task lca_megablast {
+    meta {
+        description: "Runs megablast followed by LCA for taxon identification."
+    }
+    input {
+        File    trimmed_fasta
+        File    blast_db_tgz
+        File    taxdb
+        String  db_name
+        File    taxonomy_db_tgz
+        String  fasta_basename = basename(trimmed_fasta, ".fasta")
+        Int     machine_mem_gb = 500 
+        Int     cpu = 16
+        Int     disk_size_gb = 300
+        String  docker = "quay.io/broadinstitute/viral-classify:2.2.4.2" #skip-global-version-pin
+    }
+    parameter_meta {
+        trimmed_fasta: {
+            description: "Input sequence FASTA file with clean bam reads.",
+            category: "required"
+        }
+        blast_db_tgz: {
+            description: "Compressed BLAST database.",
+            category: 'required'
+        }
+        db_name: {
+            description: "BLAST database name (default = nt).",
+            category: "other"
+        }
+        taxonomy_db_tgz: {
+            description: "Compressed taxnonomy dataset.",
+            category: "required"
+        }
+    }
+    command <<<
+    #Extract BLAST DB tarball
+    read_utils.py extract_tarball \
+      ~{blast_db_tgz} . \
+      --loglevel=DEBUG
+    
+    # Extract taxonomy DB tarball 
+    read_utils.py extract_tarball \
+      ~{taxonomy_db_tgz} . \
+      --loglevel=DEBUG
+
+    '''
+    #Extract taxid map file tarball
+    read_utils.py extract_tarball \
+        ~{taxdb} . \
+        --loglevel=DEBUG
+    '''
+
+    #Set permissions 
+    chmod +x /opt/viral-ngs/source/retrieve_top_blast_hits_LCA_for_each_sequence.pl
+    chmod +x /opt/viral-ngs/source/LCA_table_to_kraken_output_format.pl
+    # Verify BLAST database
+    blastdbcmd -db "~{db_name}" -info
+    if [ $? -ne 0 ]; then
+        echo "Database '~{db_name}' not found or is inaccessible."
+        exit 1
+    else
+        echo "Database '~{db_name}' found and accessible."
+    fi
+    #miniwdl run worked when the Title DB was same as called under db. Remade DB, make sure to note title of DB. 
+    #Log start time 
+    START_TIME=$(date +%s)
+    # Run megablast against nt
+    blastn -task megablast -query "~{trimmed_fasta}" -db "~{db_name}" -max_target_seqs 50 -num_threads `nproc` -outfmt "6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue" -out "~{fasta_basename}.fasta_megablast_nt.tsv"
+    #Log end time
+    END_TIME=$(date +%s)
+     # Calculate elapsed time
+    ELAPSED_TIME=$(($END_TIME - $START_TIME))
+    echo "BLAST step took $ELAPSED_TIME seconds." > blast_elapsed_time.txt
+    # Run LCA
+    retrieve_top_blast_hits_LCA_for_each_sequence.pl "~{fasta_basename}.fasta_megablast_nt.tsv" nodes.dmp 10 > "~{fasta_basename}.fasta_megablast_nt.tsv_LCA.txt"
+    # Run Krona output conversion 
+    LCA_table_to_kraken_output_format.pl "~{fasta_basename}.fasta_megablast_nt.tsv_LCA.txt" "~{trimmed_fasta}" > "~{fasta_basename}.kraken.tsv"
+    # Done
+>>>
+
+output {
+    File    LCA_output = "~{fasta_basename}.fasta_megablast_nt.tsv_LCA.txt"
+    File    kraken_output_fromat =  "~{fasta_basename}.kraken.tsv"
+    File    elapsed_time_normal_blastn = "blast_elapsed_time.txt"
+}
+runtime {
+    docker:docker
+    memory: machine_mem_gb + "GB"
+    cpu: cpu
+    disks: "local-disk" + disk_size_gb + "HDD"
+    dx_instance_type: "n2-highmem-16"
+}
+}
+task ChunkBlastHits {
+    meta {
+        description: "Process BLAST hits from a FASTA file by dividing the file into smaller chunks for parallel processing (blastn_chunked_fasta)."
+    }
+    input {
+        File   inFasta
+        File   blast_db_tgz
+        File?  taxidlist
+        String db_name
+        String tasks = "megablast"
+        Int    chunkSize=1000000
+        String outfmt = "6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue"
+        Int    max_target_seqs = 1
+        String output_type = "full_line"
+        String? log_dir 
+        String blast_hits_output = "~{fasta_basename}_new_output.txt"
+        Int    machine_mem_gb = 64 
+        Int    cpu = 16
+        Int    disk_size_gb = 300
+        String docker = "quay.io/broadinstitute/viral-classify:fn_blast" #skip-global-version-pin
+    }
+        String fasta_basename = basename(inFasta, ".fasta")
+        #setting current working directory as logging outputs
+        String log_dir_final = select_first([log_dir, "."])
+    command <<<
+    #Extract tarball contents
+    read_utils.py extract_tarball \
+      ~{blast_db_tgz} . \
+      --loglevel=DEBUG
+    export LOG_DIR=~{log_dir_final}
+    echo "Using $(nproc) CPU cores."
+    echo "Asked for ~{machine_mem_gb} memory GB"
+    #Adding taxidlist input as optional 
+    TAXIDLIST_OPTION=""
+    if [ -n "~{taxidlist}" ]; then
+        TAXIDLIST_OPTION="--taxidlist ~{taxidlist}"
+    fi
+    #COMMAND
+    time python /opt/viral-ngs/viral-classify/taxon_filter.py chunk_blast_hits "~{inFasta}" "~{db_name}" "~{blast_hits_output}" --outfmt '~{outfmt}' --chunkSize ~{chunkSize} --task '~{tasks}' --max_target_seqs "~{max_target_seqs}" --output_type "~{output_type}" $TAXIDLIST_OPTION
+    #add taxidlist to command only if user input
+
+    # Extract runtime
+    grep "Completed the WHOLE blastn_chunked_fasta in" ~{log_dir_final}/blast_py.log | awk '{print $NF}' > ~{log_dir_final}/duration_seconds.txt
+
+    if [ -f /sys/fs/cgroup/memory.peak ]; then 
+        cat /sys/fs/cgroup/memory.peak
+    elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then 
+        cat /sys/fs/cgroup/memory/memory.peak
+    elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then 
+        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes
+    else 
+        echo "0"
+    fi > MEM_BYTES
+    cat /proc/loadavg > CPU_LOAD
+    
+>>>
+
+output {
+    File blast_hits = "~{blast_hits_output}"
+    File blast_py_log = "~{log_dir_final}/blast_py.log"
+    File duration_seconds = "~{log_dir_final}/duration_seconds.txt"
+    Int  max_ram_gb = ceil(read_float("MEM_BYTES")/1000000000)
+    String  cpu_load = read_string("CPU_LOAD")
+}
+runtime {
+    docker: docker
+    cpu: cpu
+    memory: machine_mem_gb + " GB"
+    disks: "local-disk " + disk_size_gb + " LOCAL"
+    dx_instance_type: "n2-standard-16"
+}
+
+}
+
+task blastoff {
+    meta{
+        description:"Blastoff wrapper"
+    }
+    input{
+        File   trimmed_fasta
+        String outfmt = "6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue"
+        String tasks = "megablast"
+        Int    chunkSize=5000000
+        Int    max_target_seqs = 50
+        String output_type = "full_line"
+        String? log_dir 
+        Int     host_species = 9606
+        Int     stage2_min_id = 98
+        Int     stage2_min_qcov = 98 
+        #Are these id/qcov b/w stage 2 & 3 ever different?
+        Int     stage3_min_id = 98
+        Int     stage3_min_qcov = 98
+        File    blast_db_tgz
+        File    taxonomy_db_tgz
+        String  db_name
+        String  fasta_basename = basename(trimmed_fasta, ".fasta")
+        Int     machine_mem_gb = 64 
+        Int     cpu = 16
+        Int     disk_size_gb = 300
+        String  docker = "quay.io/broadinstitute/viral-classify:fn_cleaned_blast" #skip-global-version-pin
+
+    }
+        #setting current working directory as logging outputs
+        String log_dir_final = select_first([log_dir, "."])
+    command <<<
+    #Extract BLAST DB tarball
+    read_utils.py extract_tarball \
+      ~{blast_db_tgz} . \
+      --loglevel=DEBUG
+
+    # Extract taxonomy DB tarball (includes nodes.dmp)
+    read_utils.py extract_tarball \
+      ~{taxonomy_db_tgz} . \
+      --loglevel=DEBUG
+    
+    export LOG_DIR=~{log_dir_final}
+    #Note threads and memory asked
+    echo "Using $(nproc) CPU cores."
+    echo "Asked for ~{machine_mem_gb} memory GB"
+    #permissions 
+    chmod +x /opt/viral-ngs/source/retrieve_top_blast_hits_LCA_for_each_sequence.pl
+    chmod +x /opt/viral-ngs/source/retrieve_most_common_taxonids_in_LCA_output.pl
+    chmod +x /opt/viral-ngs/source/filter_LCA_matches.pl
+    chmod +x /opt/viral-ngs/source/add_one_value_column.pl
+    chmod +x /opt/viral-ngs/source/retrieve_sequences_appearing_or_not_appearing_in_table.pl
+    chmod +x /opt/viral-ngs/source/generate_LCA_table_for_sequences_with_no_matches.pl
+    chmod +x /opt/viral-ngs/source/concatenate_tables.pl
+    chmod +x /opt/viral-ngs/source/LCA_table_to_kraken_output_format.pl
+    chmod +x /opt/viral-ngs/source/select_random_sequences.pl
+
+
+    #STAGE 1 
+    #Subsamples 100 random reads from original FASTA file
+    select_random_sequences.pl "~{trimmed_fasta}" 100 > "~{fasta_basename}_subsampled.fasta"
+    #run megablast on random reads x nt
+    #switched output from out to txt for readability issues
+    #blastn -task megablast -query "~{fasta_basename}_subsampled.fasta"  -db "~{db_name}" -max_target_seqs 50 -num_threads `nproc` -outfmt "6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue" -out "~{fasta_basename}_subsampled.fasta_megablast_nt.tsv" 
+    python /opt/viral-ngs/viral-classify/taxon_filter.py chunk_blast_hits "~{fasta_basename}_subsampled.fasta" "~{db_name}" "~{fasta_basename}_subsampled.fasta_megablast_nt.tsv"  --outfmt '~{outfmt}' --chunkSize ~{chunkSize} --task '~{tasks}' --max_target_seqs "~{max_target_seqs}" --output_type "~{output_type}" 
+    # Run LCA
+    retrieve_top_blast_hits_LCA_for_each_sequence.pl "~{fasta_basename}_subsampled.fasta_megablast_nt.tsv" nodes.dmp 1 1 > "~{fasta_basename}_subsampled.fasta_megablast_nt.tsv_LCA.txt"
+    #Looks for most frequently matched taxon IDs and outputs a list
+    retrieve_most_common_taxonids_in_LCA_output.pl "~{fasta_basename}_subsampled.fasta_megablast_nt.tsv_LCA.txt" species 10 1 > "sample_specific_db_taxa.txt" 
+    # Create an empty sample_specific_db_taxa.txt if it doesn't exist
+    touch sample_specific_db_taxa.txt
+    #adding host_species to sample_specific_db_taxa.txt
+    echo "~{host_species}" >> "sample_specific_db_taxa.txt"
+    #ensure file is sorted and unique 
+    sort sample_specific_db_taxa.txt | uniq > sample_specific_db_taxa_unique.txt
+    mv sample_specific_db_taxa_unique.txt sample_specific_db_taxa.txt
+    echo "input sequences to stage 2:"
+    grep ">" "~{trimmed_fasta}" | wc -l
+    echo "--END STAGE 1"
+
+    #STAGE 2
+    echo "---START STAGE 2"
+    echo "megablast sample-specific database start"
+    #Run blastn w/ taxidlist specific 
+    #blastn -task megablast -query "~{fasta_basename}_subsampled.fasta" -db "~{db_name}" -max_target_seqs 50 -num_threads `nproc` -taxidlist "sample_specific_db_taxa.txt" -outfmt "6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue" -out "~{fasta_basename}_megablast_sample_specific_db.tsv" 
+    python /opt/viral-ngs/viral-classify/taxon_filter.py chunk_blast_hits "~{trimmed_fasta}" "~{db_name}" "~{fasta_basename}_megablast_sample_specific_db.tsv"  --outfmt '~{outfmt}' --chunkSize ~{chunkSize} --task '~{tasks}' --max_target_seqs "~{max_target_seqs}" --output_type "~{output_type}" --taxidlist "sample_specific_db_taxa.txt"
+    #Run LCA on last output
+    retrieve_top_blast_hits_LCA_for_each_sequence.pl "~{fasta_basename}_megablast_sample_specific_db.tsv" nodes.dmp 2 >  "~{fasta_basename}_megablast_sample_specific_db_LCA.txt" 
+    #filter
+    filter_LCA_matches.pl "~{fasta_basename}_megablast_sample_specific_db_LCA.txt" 1 0 0 "~{stage2_min_id}" 999 "~{stage2_min_qcov}" 999 > "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt"
+    #add one clmn value: database
+    add_one_value_column.pl "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt" "database" "sample-specific" > "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt_column_added.txt"
+    mv "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt_column_added.txt" "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt"
+    #add one clmn value: classified
+    add_one_value_column.pl "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt" "classified" "classified" > "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt_column_added.txt"
+    mv "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt_column_added.txt" "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt"
+    #retrieves collection of unclassified sequences
+    retrieve_sequences_appearing_or_not_appearing_in_table.pl "~{trimmed_fasta}" "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt" 0 0 > "~{fasta_basename}_megablast_sample_specific_db_unclassified.fasta"
+    # megablast_sample_specific_db_${sample_fasta}_unclassified.fasta = "~{fasta_basename}_megablast_sample_specific_db_unclassified.fasta"
+    echo "input sequences to stage 3"
+    grep ">" "~{fasta_basename}_megablast_sample_specific_db_unclassified.fasta" | wc -l 
+    echo "--END STAGE 2"
+    echo "---START STAGE 3"
+    
+    #Stage 3 
+    #/blast/results/${sample_fasta}_megablast_sample_specific_db_megablast_nt.out = "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.tsv"
+    #blastn -task megablast -query "~{fasta_basename}_megablast_sample_specific_db_unclassified.fasta" -db "~{db_name}" -max_target_seqs 50 -num_threads `nproc` -outfmt "6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue" -out "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.tsv"
+    python /opt/viral-ngs/viral-classify/taxon_filter.py chunk_blast_hits "~{fasta_basename}_megablast_sample_specific_db_unclassified.fasta" "~{db_name}" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.tsv" --outfmt '~{outfmt}' --chunkSize ~{chunkSize} --task '~{tasks}' --max_target_seqs "~{max_target_seqs}" --output_type "~{output_type}"
+    retrieve_top_blast_hits_LCA_for_each_sequence.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.tsv" nodes.dmp 10 > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt"
+    filter_LCA_matches.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt" 0 0 0 "~{stage3_min_id}" 999 "~{stage3_min_qcov}" 999 > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt_LCA_classified.txt"
+    #add one column: database, nt
+    add_one_value_column.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt_LCA_classified.txt" "database" "nt" > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_classified.txt_column_added.txt"
+    mv "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_classified.txt_column_added.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt_LCA_classified.txt"
+    #add one column: classified, classified
+    add_one_value_column.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt_LCA_classified.txt" "classified" "classified" > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_classified.txt_column_added.txt"
+    mv "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_classified.txt_column_added.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt_LCA_classified.txt"
+    filter_LCA_matches.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt" 0 0 0 "~{stage3_min_id}" 999 "~{stage3_min_qcov}" 999 1 > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt"
+    add_one_value_column.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt" "database" "nt" > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt_column_added.txt"
+    mv "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt_column_added.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt"
+    add_one_value_column.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt" "classified" "unclassified" > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt_column_added.txt"
+    mv "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt_column_added.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt"
+    generate_LCA_table_for_sequences_with_no_matches.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt" "~{fasta_basename}_megablast_sample_specific_db_unclassified.fasta" > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt"
+    add_one_value_column.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt" "database" "nt" > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt_column_added.txt"
+    mv "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt_column_added.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt" 
+    add_one_value_column.pl "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt" "classified" "unclassified (no matches)" > "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt_column_added.txt"
+    mv "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt_column_added.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt" 
+    #Table 1 (classified sequences from stage 2) "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt"
+    #Table 2 (classified sequences from stage 3) "~{fasta_basename}_megablast_sample_specific_db_megablast_nt_LCA_classified.txt"
+    #Table 3 (unclassified sequences from stage 3) "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt"
+    #Table 4 (no-blast-hits sequences from stage 3) "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt"
+    concatenate_tables.pl "~{fasta_basename}_megablast_sample_specific_LCA.txt_classified.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt_LCA_classified.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_unclassified.txt" "~{fasta_basename}_megablast_sample_specific_db_megablast_nt.out_LCA.txt_no_hits.txt" > "~{fasta_basename}_blastoff.txt"
+    awk 'BEGIN {FS="\t";OFS="\t"} {for (i=2; i<=NF; i++) printf "%s%s", $i, (i<NF ? OFS : ORS)}' "~{fasta_basename}_blastoff.txt" > blastoff_no_first_column.txt
+    mv blastoff_no_first_column.txt "~{fasta_basename}_blastoff.txt"
+
+    LCA_table_to_kraken_output_format.pl "~{fasta_basename}_blastoff.txt" "~{trimmed_fasta}" > "~{fasta_basename}_blastoff_kraken.txt"
+
+
+    if [ -f /sys/fs/cgroup/memory.peak ]; then 
+        cat /sys/fs/cgroup/memory.peak
+    elif [ -f /sys/fs/cgroup/memory/memory.peak ]; then 
+        cat /sys/fs/cgroup/memory/memory.peak
+    elif [ -f /sys/fs/cgroup/memory/memory.max_usage_in_bytes ]; then 
+        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes
+    else 
+        echo "0"
+    fi > MEM_BYTES
+    cat /proc/loadavg > CPU_LOAD
+    >>>
+    output{
+
+        File  most_popular_taxon_id = "sample_specific_db_taxa.txt"
+        File  blastoff_results = "~{fasta_basename}_blastoff.txt"
+        File  blastoff_kraken = "~{fasta_basename}_blastoff_kraken.tsv"
+        File blast_py_log = "~{log_dir_final}/blast_py.log"
+        Int  max_ram_gb = ceil(read_float("MEM_BYTES")/1000000000)
+        String  cpu_load = read_string("CPU_LOAD")
+
+    }
+    runtime{
+        docker:docker
+        memory: machine_mem_gb + "GB"
+        cpu: cpu
+        disks: "local-disk " + disk_size_gb + " HDD"
+        dx_instance_type: "n2-highmem-8"
+    }
+
+}
diff --git a/pipes/WDL/workflows/blastoff.wdl b/pipes/WDL/workflows/blastoff.wdl
new file mode 100644
index 000000000..da326d2e4
--- /dev/null
+++ b/pipes/WDL/workflows/blastoff.wdl
@@ -0,0 +1,56 @@
+version 1.0
+
+import "../tasks/tasks_megablast.wdl" as tools
+import "../tasks/tasks_metagenomics.wdl" as metagenomics
+
+workflow megablast {
+    meta {
+        description: "Runs megablast followed by LCA for taxon identification."
+        author: "Broad Viral Genomics"
+        email: "viral-ngs@broadinstitute.org"
+        allowNestedInputs: true
+    }
+    input {
+        File    inBam
+        File    clipDb
+        File    blast_db_tgz
+        File    krona_taxonomy_tab
+        File    taxonomy_db_tgz
+        Int     host_species
+        String  db_name
+        String sample_name = basename(inBam, '.bam')
+    }
+    parameter_meta {
+        krona_taxonomy_tab: {
+            description: "Krona taxonomy database containing a single file: 'taxonomy.tab' (exact name), or possibly just a compressed 'taxonomy.tab"
+            patterns: ["*.tab.zst", "*.tab.gz", "*.tab", "*.tar.gz", "*.tar.lz4", "*.tar.bz2", "*.tar.zst"]
+        }
+    }
+    call tools.trim_rmdup_subsamp {
+        input: 
+            inBam = inBam,
+            clipDb = clipDb
+    }
+    call tools.blastoff {
+        input:
+            trimmed_fasta = trim_rmdup_subsamp.trimmed_fasta, 
+            blast_db_tgz = blast_db_tgz,
+            taxonomy_db_tgz = taxonomy_db_tgz,
+            host_species = host_species,
+            db_name = db_name
+    }
+    call metagenomics.krona {
+        input: 
+            reports_txt_gz = [blastoff.blastoff_kraken],
+            krona_taxonomy_db_tgz = krona_taxonomy_tab,
+            input_type = "tsv",
+            out_basename = "~{sample_name}.krona"
+    }
+
+    output {
+        File    most_popular_taxon_id = blastoff.most_popular_taxon_id
+        File    blastoff_txt_results = blastoff.blastoff_results
+        File    blastoff_kraken = blastoff.blastoff_kraken
+        File    krona_html = krona.krona_report_html
+    }
+}
\ No newline at end of file
diff --git a/pipes/WDL/workflows/megablast_chunk.wdl b/pipes/WDL/workflows/megablast_chunk.wdl
new file mode 100644
index 000000000..de4af7379
--- /dev/null
+++ b/pipes/WDL/workflows/megablast_chunk.wdl
@@ -0,0 +1,30 @@
+version 1.0 
+
+import "../tasks/tasks_megablast.wdl" as tools
+
+workflow chunk_megablast {
+    meta {
+        description: "Chunk megablast function"
+        author: "Broad Viral Genomics"
+        email: "viral-negs@broadinstitute.org"
+        allowNestedInputs: true
+    }
+    input {
+        File    inFasta
+        File    blast_db_tgz
+        String  db_name 
+    }
+    call tools.ChunkBlastHits {
+        input: 
+            inFasta = inFasta, 
+            blast_db_tgz = blast_db_tgz,
+            db_name = db_name
+    }
+    output {
+        File    blast_hits = ChunkBlastHits.blast_hits
+        File    blast_filter_logs = ChunkBlastHits.blast_py_log
+        File    chunk_blast_runtime = ChunkBlastHits.duration_seconds
+        Int     max_ram_gb = ChunkBlastHits.max_ram_gb
+        String  cpu_load = ChunkBlastHits.cpu_load
+    }
+}