code cleanup

tasks/task_amrfinderplus.wdl

@@ -16,13 +16,6 @@ task amrfinderplus_nuc {
     date | tee DATE
     amrfinder --version | tee AMRFINDER_VERSION
 
-    # check prodigal files
-    if [[ -f "~{prodigal_faa}" ]] && [[ -f "~{prodigal_gff}" ]]; then
-      protein=true
-    else
-      protein=false
-    fi
-
     # select mash organism if avalible
     if [[ "~{mash_organism}" != "" ]]; then
       organism="~{mash_organism}"
@@ -151,7 +144,7 @@ task amrfinderplus_nuc {
     fi
 
     # checking bash variable
-    echo "amrfinder_organism is set to:" ${amrfinder_organism}
+    echo "amrfinder_organism is set to: ${amrfinder_organism}"
 
     # protein + nucleotide (activate HMM)
     if [[ -f "~{prodigal_faa}" ]] && [[ -f "~{prodigal_gff}" ]]; then

tasks/task_bbtools.wdl

@@ -17,7 +17,7 @@ task assembly_prep {
 
   command <<<
     # version control
-    echo "$(java -ea -Xmx31715m -Xms31715m -cp /bbmap/current/ jgi.BBDuk 2>&1)" | grep version > VERSION
+    java -ea -Xmx31715m -Xms31715m -cp /bbmap/current/ jgi.BBDuk 2>&1 | grep version > VERSION
 
     # PhiX cleaning   
     bbduk.sh \
@@ -85,7 +85,7 @@ task insert_size_dist {
 
   command <<<
     # version control
-    echo "$(java -ea -Xmx31715m -Xms31715m -cp /bbmap/current/ jgi.BBDuk 2>&1)" | grep version > VERSION
+    java -ea -Xmx31715m -Xms31715m -cp /bbmap/current/ jgi.BBDuk 2>&1 | grep version > VERSION
     # map reads and create histogram
     bbmap.sh \
       ref=~{reference} \
@@ -96,12 +96,12 @@ task insert_size_dist {
       maxindel=~{max_indel} \
       fast
     #parse histogram file
-    cat ~{samplename}.ihist.txt | sed '6,1006!d' > ~{samplename}.hist.txt
+    sed '6,1006!d' ~{samplename}.ihist.txt > ~{samplename}.hist.txt
     mean=$(awk -F "\t" 'NR==1 {print $2}' ~{samplename}.ihist.txt)
     median=$(awk -F "\t" 'NR==2 {print $2}' ~{samplename}.ihist.txt)
     mode=$(awk -F "\t" 'NR==3 {print $2}' ~{samplename}.ihist.txt)
     stdev=$(awk -F "\t" 'NR==4 {print $2}' ~{samplename}.ihist.txt)
-    echo $median > MEDIAN
+    echo "$median" > MEDIAN
     # create a html plot
     touch ~{samplename}.hist.html
     x=$(awk -vORS=, 'NR>1 {print $1}' "~{samplename}.hist.txt" | sed 's/,$/\n/')

tasks/task_blast.wdl

@@ -31,7 +31,7 @@ task tblastn {
     then
       echo "No blast hit!" > GENES
     else
-      echo $hits > GENES
+      echo "$hits" > GENES
     fi
   >>>
 

tasks/task_checkm2.wdl

@@ -6,8 +6,8 @@ task checkm2 {
     File checkm2_db   
     String samplename
     String docker = "staphb/checkm2:1.0.2"
-    Int? memory = 16
-    Int? cpu = 4
+    Int memory = 16
+    Int cpu = 4
   }
 
   command <<<

tasks/task_fastp.wdl

@@ -7,15 +7,15 @@ task fastp_pe {
     File? adapters
     String docker = "staphb/fastp:0.24.0"
     String samplename
-    Int? leading = 1
-    Int? front_mean_quality = 10
-    Int? trailing = 1
-    Int? tail_mean_quality = 10
-    Int? minlen = 50
-    Int? window_size = 4
-    Int? right_mean_quality = 20
-    Int? thread = 4
-    Int? read_quality = 30
+    Int leading = 1
+    Int front_mean_quality = 10
+    Int trailing = 1
+    Int tail_mean_quality = 10
+    Int minlen = 50
+    Int window_size = 4
+    Int right_mean_quality = 20
+    Int thread = 4
+    Int read_quality = 30
     }
 
 command <<<

tasks/task_json.wdl

@@ -11,10 +11,10 @@ task write_json {
     Int total_reads_trim 
     Int r1_reads 
     Int r2_reads 
-    Float? r1_q30_raw 
-    Float? r2_q30_raw 
-    Float? r1_q30_trim 
-    Float? r2_q30_trim 
+    Float r1_q30_raw 
+    Float r2_q30_raw 
+    Float r1_q30_trim 
+    Float r2_q30_trim 
     # BBtools
     String? phiX_ratio 
     # Bracken

tasks/task_mash.wdl

@@ -6,8 +6,8 @@ task predict_taxon {
     File? reference
     String samplename
     String docker = "kincekara/mash:2.3-cbird-v2.0"
-    Int? memory = 16
-    Int? cpu = 4
+    Int memory = 16
+    Int cpu = 4
   }
 
   command <<<
@@ -35,11 +35,11 @@ task predict_taxon {
     else
       taxon=$(echo "$candidate" | cut -d ' ' -f 1,2)
     fi
-    echo $taxon > TAXON
+    echo "$taxon" > TAXON
     # find ratio
     ratio=$(awk -F "\t" 'NR==1 {printf "%.2f\n",$1*100}' ~{samplename}.mash.sorted.tsv)
-    echo $ratio > RATIO
-    printf "$taxon\t$ratio\n" > ~{samplename}.top_taxon.tsv
+    echo "$ratio" > RATIO
+    printf '%s\t%s\n' "$taxon" "$ratio" > ~{samplename}.top_taxon.tsv
   >>>
 
   output {

tasks/task_mlst.wdl

@@ -8,7 +8,7 @@ task ts_mlst {
     File assembly
     String samplename
     String docker = "staphb/mlst:2.23.0-2024-12-01"
-    Int? cpu = 4
+    Int cpu = 4
     # Parameters
     # --nopath          Strip filename paths from FILE column (default OFF)
     # --scheme [X]      Don't autodetect, force this scheme on all inputs (default '')
@@ -22,7 +22,7 @@ task ts_mlst {
     Float? minscore
   }
   command <<<
-    echo $(mlst --version 2>&1) | sed 's/mlst //' | tee VERSION
+    mlst --version 2>&1 | sed 's/mlst //' | tee VERSION
 
     #create output header
     echo -e "Filename\tPubMLST_Scheme_name\tSequence_Type_(ST)\tAllele_IDs" > ~{samplename}_ts_mlst.tsv
@@ -54,8 +54,8 @@ task ts_mlst {
         fi  
     fi
 
-    echo $predicted_mlst | tee PREDICTED_MLST
-    echo $pubmlst_scheme | tee PUBMLST_SCHEME
+    echo "$predicted_mlst" | tee PREDICTED_MLST
+    echo "$pubmlst_scheme" | tee PUBMLST_SCHEME
   >>>
   output {
     File ts_mlst_results = "~{samplename}_ts_mlst.tsv"

tasks/task_plasmidfinder.wdl

@@ -5,8 +5,8 @@ task plasmidfinder {
     File assembly
     String samplename
     String docker = "kincekara/plasmidfinder:2.1.6-db_2023-03-17"
-    Float? min_coverage = 0.6
-    Float? threshold = 0.9
+    Float min_coverage = 0.6
+    Float threshold = 0.9
     }
 
   command <<<

tasks/task_taxonomy.wdl

@@ -7,16 +7,16 @@ task profile {
     File kraken2_db
     String samplename
     String docker = "staphb/bracken:2.9"
-    Int? bracken_read_len = 100
-    Int? bracken_threshold = 10
-    String? min_hit_groups = 3
-    Int? memory = 32
-    Int? cpu = 4
+    Int bracken_read_len = 100
+    Int bracken_threshold = 10
+    Int min_hit_groups = 3
+    Int memory = 32
+    Int cpu = 4
   }
 
   command <<<
     # version
-    echo $(kraken2 --version 2>&1) | sed 's/^.*Kraken version //;s/ .*$//' | tee KVERSION
+    kraken2 --version 2>&1 | sed 's/^.*Kraken version //;s/ .*$//' | tee KVERSION
     basename -s .tar.gz ~{kraken2_db} | cut -d "_" -f2,3,4 | tee K2DB
 
     # Decompress the Kraken2 database

workflows/wf_c-bird.wdl

@@ -237,10 +237,10 @@ workflow cbird_workflow {
     Int total_reads_trim = fastp_trim.total_reads_trim
     Int r1_reads =  fastp_trim.r1_reads
     Int r2_reads = fastp_trim.r2_reads
-    Float? r1_q30_raw = fastp_trim.r1_q30_raw
-    Float? r2_q30_raw = fastp_trim.r2_q30_raw
-    Float? r1_q30_trim = fastp_trim.r1_q30_trim
-    Float? r2_q30_trim = fastp_trim.r2_q30_trim
+    Float r1_q30_raw = fastp_trim.r1_q30_raw
+    Float r2_q30_raw = fastp_trim.r2_q30_raw
+    Float r1_q30_trim = fastp_trim.r1_q30_trim
+    Float r2_q30_trim = fastp_trim.r2_q30_trim
     # BBtools
     File? phiX_stats = assembly_prep.phiX_stats
     String? bbtools_docker = assembly_prep.bbtools_docker