Adding task file for lydia's megablast tool

pipes/WDL/tasks/tasks_megablast.wdl

@@ -0,0 +1,62 @@
+version 1.0
+
+task megablast {
+    meta {
+        description: "Megablast "
+    }
+    input {
+        File    reads_bam
+        File    blast_db_tgz
+        File    taxonomy_db_tgz
+        String  bam_basename = basename(reads_bam, ".bam")
+        Int     machine_mem_gb = 128 
+        Int     cpu = 16
+        Int     disk_size_gb = 300
+        String  docker = "insert_docker_image"
+    }
+    command <<<
+    set -ex o pipefail
+    #samtools [BAM -> FASTA]
+    SAMPLENAME=$(basename reads_bam .bam | perl -lape 's/[_]/-/g')
+    echo $SAMPLENAME
+    samtools fasta -F 4 reads_bam > "$SAMPLENAME.fasta"
+    # Make directories
+    cd ; mkdir -p blastdb queries fasta results blastdb_custom
+    # Move input into queries directory
+    mv "$SAMPLENAME.fasta" queries
+    # [REMOVED] Download nt (15 minutes) - should be already added from the Docker?
+    # Run megablast against nt
+    docker run \
+    -v $HOME/blastdb:/blast/blastdb:ro -v $HOME/blastdb_custom:/blast/blastdb_custom:ro \
+    -v $HOME/queries:/blast/queries:ro \
+    -v $HOME/results:/blast/results:rw \
+    ncbi/blast \
+    blastn -task megablast -query /blast/queries/sample.fasta -db "nt" -max_target_seqs 50 -num_threads 8 \
+    -outfmt "6 qseqid sacc stitle staxids sscinames sskingdoms qlen slen length pident qcovs evalue" \
+    -out /blast/results/sample.fasta_megablast_nt.out
+
+    # Download nodes.dmp into taxdump directory
+    cd ; mkdir taxdump ; cd taxdump
+    curl ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz > taxdump.tar.gz
+    tar -xf taxdump.tar.gz
+    cd
+    ​
+    # Run LCA
+    perl retrieve_top_blast_hits_LCA_for_each_sequence.pl results/sample.fasta_megablast_nt.out taxdump/nodes.dmp 10 > results/sample.fasta_megablast_nt.out_LCA.txt
+    ​
+    # Done
+>>>
+
+output {
+    File    LCA_output = "~{bam_basename}_LCA.txt"
+    File    sample_fasta = "sample.fasta"
+}
+runtime {
+    docker:docker
+    memory: machine_mem_gb + "GB"
+    cpu: cpu
+    disks: "local-disk" + disk_size_gb + "LOCAL"
+    instance_type: "n2-highmem-16"
+#do we want to add max retries here?
+}
+}