TheiaCoV_ONT_PHB Influenza Track (#233)

* adding flu ont task

* update input JSON "read1" instead of "demultiplexed_reads"

* updated irma docker image to v1.1.3

* added seq_method as input to irma task

tasks/assembly/task_irma.wdl

@@ -3,12 +3,12 @@ version 1.0
 task irma {
   input {
     File read1
-    File read2
+    File? read2
+    String seq_method
     String samplename
     Boolean keep_ref_deletions = true
-    String irma_module = "FLU"
     String read_basename = basename(read1)
-    String docker = "us-docker.pkg.dev/general-theiagen/staphb/irma:1.0.3"
+    String docker = "cdcgov/irma:v1.1.3"
     Int memory = 8
     Int cpu = 4
     Int disk_size = 100
@@ -17,7 +17,9 @@ task irma {
     date | tee DATE
     #capture reads as bash variables
     read1=~{read1}
-    read2=~{read2}
+    if [[ "~{read2}" ]]; then 
+      read2=~{read2}
+    fi
     # set cat command based on compression
     if [[ "~{read1}" == *".gz" ]] ; then
       cat_reads="zcat"
@@ -38,15 +40,20 @@ task irma {
       echo "Read headers may lead to IRMA failure; reformatting to meet IRMA input requirements"
       sra_id=$(echo "~{read_basename}" | awk -F "_" '{ print $1 }')
       eval "${cat_reads} ~{read1}" | awk '{print (NR%4 == 1) ? "@'${sra_id}'-" ++i " 1:1" : $0}' | gzip -c > "${sra_id}-irmafix_R1.fastq.gz"
-      eval "${cat_reads} ~{read2}" | awk '{print (NR%4 == 1) ? "@'${sra_id}'-" ++i " 2:2" : $0}' | gzip -c > "${sra_id}-irmafix_R2.fastq.gz"
-      #modify read variables
       read1="${sra_id}-irmafix_R1.fastq.gz"
-      read2="${sra_id}-irmafix_R2.fastq.gz"
+      if [[ "~{read2}" ]]; then 
+        eval "${cat_reads} ~{read2}" | awk '{print (NR%4 == 1) ? "@'${sra_id}'-" ++i " 2:2" : $0}' | gzip -c > "${sra_id}-irmafix_R2.fastq.gz"
+        read2="${sra_id}-irmafix_R2.fastq.gz"
+      fi     
     else
       echo "Read headers match IRMA formatting requirements"
     fi
-    # run IRMA 
-    IRMA "~{irma_module}" "${read1}" "${read2}" ~{samplename}
+    # set IRMA module depending on sequencing technology
+    if [[ ~{seq_method} == "OXFORD_NANOPORE" ]]; then
+      IRMA "FLU-minion" "${read1}" ~{samplename}
+    else
+      IRMA "FLU" "${read1}" "${read2}" ~{samplename}
+    fi
     # capture IRMA type
     if compgen -G "~{samplename}/*fasta"; then
       echo "Type_"$(basename "$(echo "$(find ~{samplename}/*.fasta | head -n1)")" | cut -d_ -f1) > IRMA_TYPE
@@ -102,4 +109,4 @@ task irma {
     maxRetries: 3
     preemptible:  0
   }
-}
+}

tests/inputs/theiacov/wf_theiacov_ont.json

@@ -1,5 +1,5 @@
 {
     "theiacov_ont.samplename": "ont",
-    "theiacov_ont.demultiplexed_reads": "tests/data/theiacov/fastqs/ont/ont.fastq.gz",
+    "theiacov_ont.read1": "tests/data/theiacov/fastqs/ont/ont.fastq.gz",
     "theiacov_ont.primer_bed": "tests/data/theiacov/primers/artic-v3.primers.bed"
 }

workflows/theiacov/wf_theiacov_illumina_pe.wdl

@@ -133,6 +133,7 @@ workflow theiacov_illumina_pe {
             read1 = read_QC_trim.read1_clean,
             read2 = read_QC_trim.read2_clean,
             samplename = samplename,
+            seq_method = seq_method
         }
         if (defined(irma.irma_assemblies)) {
           call abricate.abricate_flu {