diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl
index 081176b48..b2ff9711c 100644
--- a/pipes/WDL/tasks/tasks_assembly.wdl
+++ b/pipes/WDL/tasks/tasks_assembly.wdl
@@ -27,34 +27,34 @@ task assemble {
 
         assembly.py --version | tee VERSION
 
-        if [[ "${assembler}" == "spades" ]]; then
+        if [[ "~{assembler}" == "spades" ]]; then
           assembly.py assemble_spades \
-            ${reads_unmapped_bam} \
-            ${trim_clip_db} \
-            ${sample_name}.assembly1-${assembler}.fasta \
-            ${'--nReads=' + spades_n_reads} \
-            ${true="--alwaysSucceed" false="" always_succeed} \
-            ${'--minContigLen=' + spades_min_contig_len} \
+            ~{reads_unmapped_bam} \
+            ~{trim_clip_db} \
+            ~{sample_name}.assembly1-~{assembler}.fasta \
+            ~{'--nReads=' + spades_n_reads} \
+            ~{true="--alwaysSucceed" false="" always_succeed} \
+            ~{'--minContigLen=' + spades_min_contig_len} \
             --memLimitGb $mem_in_gb \
-            --outReads=${sample_name}.subsamp.bam \
+            --outReads=~{sample_name}.subsamp.bam \
             --loglevel=DEBUG
         else
-          echo "unrecognized assembler ${assembler}" >&2
+          echo "unrecognized assembler ~{assembler}" >&2
           exit 1
         fi
 
-        samtools view -c ${sample_name}.subsamp.bam | tee subsample_read_count >&2
+        samtools view -c ~{sample_name}.subsamp.bam | tee subsample_read_count >&2
     }
 
     output {
-        File   contigs_fasta        = "${sample_name}.assembly1-${assembler}.fasta"
-        File   subsampBam           = "${sample_name}.subsamp.bam"
+        File   contigs_fasta        = "~{sample_name}.assembly1-~{assembler}.fasta"
+        File   subsampBam           = "~{sample_name}.subsamp.bam"
         Int    subsample_read_count = read_int("subsample_read_count")
         String viralngs_version     = read_string("VERSION")
     }
 
     runtime {
-        docker: "${docker}"
+        docker: docker
         memory: select_first([machine_mem_gb, 15]) + " GB"
         cpu: 4
         disks: "local-disk 375 LOCAL"
@@ -96,53 +96,53 @@ task scaffold {
         assembly.py --version | tee VERSION
 
         assembly.py order_and_orient \
-          ${contigs_fasta} \
-          ${sep=' ' reference_genome_fasta} \
-          ${sample_name}.intermediate_scaffold.fasta \
-          ${'--maxgap=' + nucmer_max_gap} \
-          ${'--minmatch=' + nucmer_min_match} \
-          ${'--mincluster=' + nucmer_min_cluster} \
-          ${'--min_pct_contig_aligned=' + scaffold_min_pct_contig_aligned} \
-          --outReference ${sample_name}.scaffolding_chosen_ref.fasta \
-          --outStats ${sample_name}.scaffolding_stats.txt \
-          --outAlternateContigs ${sample_name}.scaffolding_alt_contigs.fasta \
+          ~{contigs_fasta} \
+          ~{sep=' ' reference_genome_fasta} \
+          ~{sample_name}.intermediate_scaffold.fasta \
+          ~{'--maxgap=' + nucmer_max_gap} \
+          ~{'--minmatch=' + nucmer_min_match} \
+          ~{'--mincluster=' + nucmer_min_cluster} \
+          ~{'--min_pct_contig_aligned=' + scaffold_min_pct_contig_aligned} \
+          --outReference ~{sample_name}.scaffolding_chosen_ref.fasta \
+          --outStats ~{sample_name}.scaffolding_stats.txt \
+          --outAlternateContigs ~{sample_name}.scaffolding_alt_contigs.fasta \
           --loglevel=DEBUG
 
-        grep '^>' ${sample_name}.scaffolding_chosen_ref.fasta | cut -c 2- | tr '\n' '\t' > ${sample_name}.scaffolding_chosen_ref.txt
+        grep '^>' ~{sample_name}.scaffolding_chosen_ref.fasta | cut -c 2- | tr '\n' '\t' > ~{sample_name}.scaffolding_chosen_ref.txt
 
         assembly.py gapfill_gap2seq \
-          ${sample_name}.intermediate_scaffold.fasta \
-          ${reads_bam} \
-          ${sample_name}.intermediate_gapfill.fasta \
+          ~{sample_name}.intermediate_scaffold.fasta \
+          ~{reads_bam} \
+          ~{sample_name}.intermediate_gapfill.fasta \
           --memLimitGb $mem_in_gb \
           --maskErrors \
           --loglevel=DEBUG
 
-        grep -v '^>' ${sample_name}.intermediate_gapfill.fasta | tr -d '\n' | wc -c | tee assembly_preimpute_length
-        grep -v '^>' ${sample_name}.intermediate_gapfill.fasta | tr -d '\nNn' | wc -c | tee assembly_preimpute_length_unambiguous
+        grep -v '^>' ~{sample_name}.intermediate_gapfill.fasta | tr -d '\n' | wc -c | tee assembly_preimpute_length
+        grep -v '^>' ~{sample_name}.intermediate_gapfill.fasta | tr -d '\nNn' | wc -c | tee assembly_preimpute_length_unambiguous
 
         assembly.py impute_from_reference \
-          ${sample_name}.intermediate_gapfill.fasta \
-          ${sample_name}.scaffolding_chosen_ref.fasta \
-          ${sample_name}.scaffolded_imputed.fasta \
-          --newName ${sample_name} \
-          ${'--replaceLength=' + replace_length} \
-          ${'--minLengthFraction=' + min_length_fraction} \
-          ${'--minUnambig=' + min_unambig} \
-          ${'--aligner=' + aligner} \
+          ~{sample_name}.intermediate_gapfill.fasta \
+          ~{sample_name}.scaffolding_chosen_ref.fasta \
+          ~{sample_name}.scaffolded_imputed.fasta \
+          --newName ~{sample_name} \
+          ~{'--replaceLength=' + replace_length} \
+          ~{'--minLengthFraction=' + min_length_fraction} \
+          ~{'--minUnambig=' + min_unambig} \
+          ~{'--aligner=' + aligner} \
           --loglevel=DEBUG
     }
 
     output {
-        File   scaffold_fasta                        = "${sample_name}.scaffolded_imputed.fasta"
-        File   intermediate_scaffold_fasta           = "${sample_name}.intermediate_scaffold.fasta"
-        File   intermediate_gapfill_fasta            = "${sample_name}.intermediate_gapfill.fasta"
+        File   scaffold_fasta                        = "~{sample_name}.scaffolded_imputed.fasta"
+        File   intermediate_scaffold_fasta           = "~{sample_name}.intermediate_scaffold.fasta"
+        File   intermediate_gapfill_fasta            = "~{sample_name}.intermediate_gapfill.fasta"
         Int    assembly_preimpute_length             = read_int("assembly_preimpute_length")
         Int    assembly_preimpute_length_unambiguous = read_int("assembly_preimpute_length_unambiguous")
-        String scaffolding_chosen_ref_name           = read_string("${sample_name}.scaffolding_chosen_ref.txt")
-        File   scaffolding_chosen_ref                = "${sample_name}.scaffolding_chosen_ref.fasta"
-        File   scaffolding_stats                     = "${sample_name}.scaffolding_stats.txt"
-        File   scaffolding_alt_contigs               = "${sample_name}.scaffolding_alt_contigs.fasta"
+        String scaffolding_chosen_ref_name           = read_string("~{sample_name}.scaffolding_chosen_ref.txt")
+        File   scaffolding_chosen_ref                = "~{sample_name}.scaffolding_chosen_ref.fasta"
+        File   scaffolding_stats                     = "~{sample_name}.scaffolding_stats.txt"
+        File   scaffolding_alt_contigs               = "~{sample_name}.scaffolding_alt_contigs.fasta"
         String viralngs_version                      = read_string("VERSION")
     }
 
@@ -185,18 +185,18 @@ task ivar_trim {
 
     command {
         ivar version | head -1 | tee VERSION
-        if [ -f "${trim_coords_bed}" ]; then
+        if [ -f "~{trim_coords_bed}" ]; then
           ivar trim -e \
-            ${'-b ' + trim_coords_bed} \
-            ${'-m ' + min_keep_length} \
-            ${'-s ' + sliding_window} \
-            ${'-q ' + min_quality} \
-            ${'-x ' + primer_offset} \
-            -i ${aligned_bam} -p trim | tee IVAR_OUT
-          samtools sort -@ $(nproc) -m 1000M -o ${bam_basename}.trimmed.bam trim.bam
+            ~{'-b ' + trim_coords_bed} \
+            ~{'-m ' + min_keep_length} \
+            ~{'-s ' + sliding_window} \
+            ~{'-q ' + min_quality} \
+            ~{'-x ' + primer_offset} \
+            -i ~{aligned_bam} -p trim | tee IVAR_OUT
+          samtools sort -@ $(nproc) -m 1000M -o ~{bam_basename}.trimmed.bam trim.bam
         else
           echo "skipping ivar trim"
-          cp "${aligned_bam}" "${bam_basename}.trimmed.bam"
+          cp "~{aligned_bam}" "~{bam_basename}.trimmed.bam"
           echo "Trimmed primers from 0% (0) of reads." > IVAR_OUT
         fi
         PCT=$(grep "Trimmed primers from" IVAR_OUT | perl -lape 's/Trimmed primers from (\S+)%.*/$1/')
@@ -205,14 +205,14 @@ task ivar_trim {
     }
 
     output {
-        File   aligned_trimmed_bam         = "${bam_basename}.trimmed.bam"
+        File   aligned_trimmed_bam         = "~{bam_basename}.trimmed.bam"
         Float  primer_trimmed_read_percent = read_float("IVAR_TRIM_PCT")
         Int    primer_trimmed_read_count   = read_int("IVAR_TRIM_COUNT")
         String ivar_version                = read_string("VERSION")
     }
 
     runtime {
-        docker: "${docker}"
+        docker: docker
         memory: select_first([machine_mem_gb, 7]) + " GB"
         cpu: 4
         disks: "local-disk 375 LOCAL"
@@ -270,7 +270,7 @@ task ivar_trim_stats {
     }
 
     runtime {
-        docker: "${docker}"
+        docker: docker
         memory: "1 GB"
         cpu: 1
         disks: "local-disk 50 HDD"
@@ -304,77 +304,77 @@ task align_reads {
     aligner: { description: "Short read aligner to use: novoalign, minimap2, or bwa. (Default: novoalign)" }
   }
   
-  command {
+  command <<<
     set -ex # do not set pipefail, since grep exits 1 if it can't find the pattern
 
     read_utils.py --version | tee VERSION
 
     mem_in_mb=$(/opt/viral-ngs/source/docker/calc_mem.py mb 90)
 
-    cp ${reference_fasta} assembly.fasta
+    cp "~{reference_fasta}" assembly.fasta
     grep -v '^>' assembly.fasta | tr -d '\n' | wc -c | tee assembly_length
 
     if [ "$(cat assembly_length)" != "0" ]; then
 
       # only perform the following if the reference is non-empty
 
-      if [ "${aligner}" == "novoalign" ]; then
+      if [ "~{aligner}" == "novoalign" ]; then
         read_utils.py novoindex \
           assembly.fasta \
-          ${"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
+          ~{"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
           --loglevel=DEBUG
       fi
       read_utils.py index_fasta_picard assembly.fasta --loglevel=DEBUG
       read_utils.py index_fasta_samtools assembly.fasta --loglevel=DEBUG
 
       read_utils.py align_and_fix \
-        ${reads_unmapped_bam} \
+        "~{reads_unmapped_bam}" \
         assembly.fasta \
-        --outBamAll "${sample_name}.all.bam" \
-        --outBamFiltered "${sample_name}.mapped.bam" \
-        --aligner ${aligner} \
-        ${'--aligner_options "' + aligner_options + '"'} \
-        ${true='--skipMarkDupes' false="" skip_mark_dupes} \
+        --outBamAll "~{sample_name}.all.bam" \
+        --outBamFiltered "~{sample_name}.mapped.bam" \
+        --aligner ~{aligner} \
+        ~{'--aligner_options "' + aligner_options + '"'} \
+        ~{true='--skipMarkDupes' false="" skip_mark_dupes} \
         --JVMmemory "$mem_in_mb"m \
-        ${"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
+        ~{"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
         --loglevel=DEBUG
 
     else
       # handle special case of empty reference fasta -- emit empty bams (with original bam headers)
-      samtools view -H -b "${reads_unmapped_bam}" > "${sample_name}.all.bam"
-      samtools view -H -b "${reads_unmapped_bam}" > "${sample_name}.mapped.bam"
+      samtools view -H -b "~{reads_unmapped_bam}" > "~{sample_name}.all.bam"
+      samtools view -H -b "~{reads_unmapped_bam}" > "~{sample_name}.mapped.bam"
 
-      samtools index "${sample_name}.all.bam" "${sample_name}.all.bai"
-      samtools index "${sample_name}.mapped.bam" "${sample_name}.mapped.bai"
+      samtools index "~{sample_name}.all.bam" "~{sample_name}.all.bai"
+      samtools index "~{sample_name}.mapped.bam" "~{sample_name}.mapped.bai"
     fi
 
     cat /proc/loadavg > CPU_LOAD
 
     # collect figures of merit
     grep -v '^>' assembly.fasta | tr -d '\nNn' | wc -c | tee assembly_length_unambiguous
-    samtools view -c ${reads_unmapped_bam} | tee reads_provided
-    samtools view -c ${sample_name}.mapped.bam | tee reads_aligned
+    samtools view -c "~{reads_unmapped_bam}" | tee reads_provided
+    samtools view -c "~{sample_name}.mapped.bam" | tee reads_aligned
     # report only primary alignments 260=exclude unaligned reads and secondary mappings
-    samtools view -h -F 260 ${sample_name}.all.bam | samtools flagstat - | tee ${sample_name}.all.bam.flagstat.txt
-    grep properly ${sample_name}.all.bam.flagstat.txt | cut -f 1 -d ' ' | tee read_pairs_aligned
-    samtools view ${sample_name}.mapped.bam | cut -f10 | tr -d '\n' | wc -c | tee bases_aligned
+    samtools view -h -F 260 "~{sample_name}.all.bam" | samtools flagstat - | tee ~{sample_name}.all.bam.flagstat.txt
+    grep properly "~{sample_name}.all.bam.flagstat.txt" | cut -f 1 -d ' ' | tee read_pairs_aligned
+    samtools view "~{sample_name}.mapped.bam" | cut -f10 | tr -d '\n' | wc -c | tee bases_aligned
     python -c "print (float("$(cat bases_aligned)")/"$(cat assembly_length_unambiguous)") if "$(cat assembly_length_unambiguous)">0 else print(0)" > mean_coverage
 
     # fastqc mapped bam
-    reports.py fastqc ${sample_name}.mapped.bam ${sample_name}.mapped_fastqc.html --out_zip ${sample_name}.mapped_fastqc.zip
+    reports.py fastqc ~{sample_name}.mapped.bam ~{sample_name}.mapped_fastqc.html --out_zip ~{sample_name}.mapped_fastqc.zip
 
     cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
-    cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-  }
+    { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+  >>>
 
   output {
-    File   aligned_bam                   = "${sample_name}.all.bam"
-    File   aligned_bam_idx               = "${sample_name}.all.bai"
-    File   aligned_bam_flagstat          = "${sample_name}.all.bam.flagstat.txt"
-    File   aligned_only_reads_bam        = "${sample_name}.mapped.bam"
-    File   aligned_only_reads_bam_idx    = "${sample_name}.mapped.bai"
-    File   aligned_only_reads_fastqc     = "${sample_name}.mapped_fastqc.html"
-    File   aligned_only_reads_fastqc_zip = "${sample_name}.mapped_fastqc.zip"
+    File   aligned_bam                   = "~{sample_name}.all.bam"
+    File   aligned_bam_idx               = "~{sample_name}.all.bai"
+    File   aligned_bam_flagstat          = "~{sample_name}.all.bam.flagstat.txt"
+    File   aligned_only_reads_bam        = "~{sample_name}.mapped.bam"
+    File   aligned_only_reads_bam_idx    = "~{sample_name}.mapped.bai"
+    File   aligned_only_reads_fastqc     = "~{sample_name}.mapped_fastqc.html"
+    File   aligned_only_reads_fastqc_zip = "~{sample_name}.mapped_fastqc.zip"
     Int    reads_provided                = read_int("reads_provided")
     Int    reads_aligned                 = read_int("reads_aligned")
     Int    read_pairs_aligned            = read_int("read_pairs_aligned")
@@ -387,7 +387,7 @@ task align_reads {
   }
 
   runtime {
-    docker: "${docker}"
+    docker: docker
     memory: select_first([machine_mem_gb, 15]) + " GB"
     cpu: 8
     disks: "local-disk 375 LOCAL"
@@ -432,26 +432,26 @@ task refine_assembly_with_aligned_reads {
 
         assembly.py --version | tee VERSION
 
-        if [ ${true='true' false='false' mark_duplicates} == "true" ]; then
+        if [ ~{true='true' false='false' mark_duplicates} == "true" ]; then
           read_utils.py mkdup_picard \
-            ${reads_aligned_bam} \
+            ~{reads_aligned_bam} \
             temp_markdup.bam \
             --JVMmemory "$mem_in_mb"m \
             --loglevel=DEBUG
         else
-          ln -s ${reads_aligned_bam} temp_markdup.bam
+          ln -s ~{reads_aligned_bam} temp_markdup.bam
         fi
         samtools index -@ $(nproc) temp_markdup.bam temp_markdup.bai
 
-        ln -s ${reference_fasta} assembly.fasta
+        ln -s ~{reference_fasta} assembly.fasta
         assembly.py refine_assembly \
           assembly.fasta \
           temp_markdup.bam \
           refined.fasta \
           --already_realigned_bam=temp_markdup.bam \
-          --outVcf ${sample_name}.sites.vcf.gz \
-          --min_coverage ${min_coverage} \
-          --major_cutoff ${major_cutoff} \
+          --outVcf ~{sample_name}.sites.vcf.gz \
+          --min_coverage ~{min_coverage} \
+          --major_cutoff ~{major_cutoff} \
           --JVMmemory "$mem_in_mb"m \
           --loglevel=DEBUG
 
@@ -487,7 +487,7 @@ task refine_assembly_with_aligned_reads {
     }
 
     runtime {
-        docker: "${docker}"
+        docker: docker
         memory: select_first([machine_mem_gb, 15]) + " GB"
         cpu: 8
         disks: "local-disk 375 LOCAL"
@@ -551,7 +551,7 @@ task refine {
     }
 
     runtime {
-        docker: "${docker}"
+        docker: docker
         memory: select_first([machine_mem_gb, 7]) + " GB"
         cpu: 8
         disks: "local-disk 375 LOCAL"
@@ -597,95 +597,95 @@ task refine_2x_and_plot {
 
         assembly.py --version | tee VERSION
 
-        ln -s ${assembly_fasta} assembly.fasta
+        ln -s ~{assembly_fasta} assembly.fasta
         read_utils.py novoindex \
         assembly.fasta \
-        ${"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
+        ~{"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
         --loglevel=DEBUG
 
         # refine 1
         assembly.py refine_assembly \
           assembly.fasta \
-          ${reads_unmapped_bam} \
-          ${sample_name}.refine1.fasta \
-          --outVcf ${sample_name}.refine1.pre_fasta.vcf.gz \
-          --min_coverage ${refine1_min_coverage} \
-          --major_cutoff ${refine1_major_cutoff} \
-          --novo_params="${refine1_novoalign_options}" \
+          ~{reads_unmapped_bam} \
+          ~{sample_name}.refine1.fasta \
+          --outVcf ~{sample_name}.refine1.pre_fasta.vcf.gz \
+          --min_coverage ~{refine1_min_coverage} \
+          --major_cutoff ~{refine1_major_cutoff} \
+          --novo_params="~{refine1_novoalign_options}" \
           --JVMmemory "$mem_in_mb"m \
-          ${"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
+          ~{"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
           --loglevel=DEBUG
 
         # refine 2
         assembly.py refine_assembly \
-          ${sample_name}.refine1.fasta \
-          ${reads_unmapped_bam} \
-          ${sample_name}.fasta \
-          --outVcf ${sample_name}.refine2.pre_fasta.vcf.gz \
-          --min_coverage ${refine2_min_coverage} \
-          --major_cutoff ${refine2_major_cutoff} \
-          --novo_params="${refine2_novoalign_options}" \
-          ${"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
+          ~{sample_name}.refine1.fasta \
+          ~{reads_unmapped_bam} \
+          ~{sample_name}.fasta \
+          --outVcf ~{sample_name}.refine2.pre_fasta.vcf.gz \
+          --min_coverage ~{refine2_min_coverage} \
+          --major_cutoff ~{refine2_major_cutoff} \
+          --novo_params="~{refine2_novoalign_options}" \
+          ~{"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
           --JVMmemory "$mem_in_mb"m \
           --loglevel=DEBUG
 
         # final alignment
         read_utils.py align_and_fix \
-          ${reads_unmapped_bam} \
-          ${sample_name}.fasta \
-          --outBamAll ${sample_name}.all.bam \
-          --outBamFiltered ${sample_name}.mapped.bam \
-          --aligner_options "${plot_coverage_novoalign_options}" \
+          ~{reads_unmapped_bam} \
+          ~{sample_name}.fasta \
+          --outBamAll ~{sample_name}.all.bam \
+          --outBamFiltered ~{sample_name}.mapped.bam \
+          --aligner_options "~{plot_coverage_novoalign_options}" \
           --JVMmemory "$mem_in_mb"m \
-          ${"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
+          ~{"--NOVOALIGN_LICENSE_PATH=" + novocraft_license} \
           --loglevel=DEBUG
 
         # collect figures of merit
         set +o pipefail # grep will exit 1 if it fails to find the pattern
-        grep -v '^>' ${sample_name}.fasta | tr -d '\n' | wc -c | tee assembly_length
-        grep -v '^>' ${sample_name}.fasta | tr -d '\nNn' | wc -c | tee assembly_length_unambiguous
-        samtools view -c ${sample_name}.mapped.bam | tee reads_aligned
+        grep -v '^>' ~{sample_name}.fasta | tr -d '\n' | wc -c | tee assembly_length
+        grep -v '^>' ~{sample_name}.fasta | tr -d '\nNn' | wc -c | tee assembly_length_unambiguous
+        samtools view -c ~{sample_name}.mapped.bam | tee reads_aligned
         # report only primary alignments 260=exclude unaligned reads and secondary mappings
-        samtools view -h -F 260 ${sample_name}.all.bam | samtools flagstat - | tee ${sample_name}.all.bam.flagstat.txt
-        grep properly ${sample_name}.all.bam.flagstat.txt | cut -f 1 -d ' ' | tee read_pairs_aligned
-        samtools view ${sample_name}.mapped.bam | cut -f10 | tr -d '\n' | wc -c | tee bases_aligned
+        samtools view -h -F 260 ~{sample_name}.all.bam | samtools flagstat - | tee ~{sample_name}.all.bam.flagstat.txt
+        grep properly ~{sample_name}.all.bam.flagstat.txt | cut -f 1 -d ' ' | tee read_pairs_aligned
+        samtools view ~{sample_name}.mapped.bam | cut -f10 | tr -d '\n' | wc -c | tee bases_aligned
         #echo $(( $(cat bases_aligned) / $(cat assembly_length) )) | tee mean_coverage
         python -c "print (float("$(cat bases_aligned)")/"$(cat assembly_length)") if "$(cat assembly_length)">0 else print(0)" > mean_coverage
 
         # fastqc mapped bam
-        reports.py fastqc ${sample_name}.mapped.bam ${sample_name}.mapped_fastqc.html --out_zip ${sample_name}.mapped_fastqc.zip
+        reports.py fastqc ~{sample_name}.mapped.bam ~{sample_name}.mapped_fastqc.html --out_zip ~{sample_name}.mapped_fastqc.zip
 
         # plot coverage
         if [ $(cat reads_aligned) != 0 ]; then
           reports.py plot_coverage \
-            ${sample_name}.mapped.bam \
-            ${sample_name}.coverage_plot.pdf \
-            --outSummary "${sample_name}.coverage_plot.txt" \
+            ~{sample_name}.mapped.bam \
+            ~{sample_name}.coverage_plot.pdf \
+            --outSummary "~{sample_name}.coverage_plot.txt" \
             --plotFormat pdf \
             --plotWidth 1100 \
             --plotHeight 850 \
             --plotDPI 100 \
-            --plotTitle "${sample_name} coverage plot" \
+            --plotTitle "~{sample_name} coverage plot" \
             --loglevel=DEBUG
         else
-          touch ${sample_name}.coverage_plot.pdf ${sample_name}.coverage_plot.txt
+          touch ~{sample_name}.coverage_plot.pdf ~{sample_name}.coverage_plot.txt
         fi
     }
 
     output {
-        File   refine1_sites_vcf_gz          = "${sample_name}.refine1.pre_fasta.vcf.gz"
-        File   refine1_assembly_fasta        = "${sample_name}.refine1.fasta"
-        File   refine2_sites_vcf_gz          = "${sample_name}.refine2.pre_fasta.vcf.gz"
-        File   final_assembly_fasta          = "${sample_name}.fasta"
-        File   aligned_bam                   = "${sample_name}.all.bam"
-        File   aligned_bam_idx               = "${sample_name}.all.bai"
-        File   aligned_bam_flagstat          = "${sample_name}.all.bam.flagstat.txt"
-        File   aligned_only_reads_bam        = "${sample_name}.mapped.bam"
-        File   aligned_only_reads_bam_idx    = "${sample_name}.mapped.bai"
-        File   aligned_only_reads_fastqc     = "${sample_name}.mapped_fastqc.html"
-        File   aligned_only_reads_fastqc_zip = "${sample_name}.mapped_fastqc.zip"
-        File   coverage_plot                 = "${sample_name}.coverage_plot.pdf"
-        File   coverage_tsv                  = "${sample_name}.coverage_plot.txt"
+        File   refine1_sites_vcf_gz          = "~{sample_name}.refine1.pre_fasta.vcf.gz"
+        File   refine1_assembly_fasta        = "~{sample_name}.refine1.fasta"
+        File   refine2_sites_vcf_gz          = "~{sample_name}.refine2.pre_fasta.vcf.gz"
+        File   final_assembly_fasta          = "~{sample_name}.fasta"
+        File   aligned_bam                   = "~{sample_name}.all.bam"
+        File   aligned_bam_idx               = "~{sample_name}.all.bai"
+        File   aligned_bam_flagstat          = "~{sample_name}.all.bam.flagstat.txt"
+        File   aligned_only_reads_bam        = "~{sample_name}.mapped.bam"
+        File   aligned_only_reads_bam_idx    = "~{sample_name}.mapped.bai"
+        File   aligned_only_reads_fastqc     = "~{sample_name}.mapped_fastqc.html"
+        File   aligned_only_reads_fastqc_zip = "~{sample_name}.mapped_fastqc.zip"
+        File   coverage_plot                 = "~{sample_name}.coverage_plot.pdf"
+        File   coverage_tsv                  = "~{sample_name}.coverage_plot.txt"
         Int    assembly_length               = read_int("assembly_length")
         Int    assembly_length_unambiguous   = read_int("assembly_length_unambiguous")
         Int    reads_aligned                 = read_int("reads_aligned")
@@ -696,7 +696,7 @@ task refine_2x_and_plot {
     }
 
     runtime {
-        docker: "${docker}"
+        docker: docker
         memory: select_first([machine_mem_gb, 7]) + " GB"
         cpu: 8
         disks: "local-disk 375 LOCAL"
@@ -727,7 +727,7 @@ task run_discordance {
         # create 2-col table with read group ids in both cols
         python3 <<CODE
         import tools.samtools
-        header = tools.samtools.SamtoolsTool().getHeader("${reads_aligned_bam}")
+        header = tools.samtools.SamtoolsTool().getHeader("~{reads_aligned_bam}")
         rgids = [[x[3:] for x in h if x.startswith('ID:')][0] for h in header if h[0]=='@RG']
         n_rgs = len(rgids)
         with open('readgroups.txt', 'wt') as outf:
@@ -744,24 +744,24 @@ task run_discordance {
         bcftools mpileup \
           -G readgroups.txt -d 10000 -a "FORMAT/DP,FORMAT/AD" \
           -q 1 -m 2 -Ou \
-          -f "${reference_fasta}" "${reads_aligned_bam}" \
+          -f "~{reference_fasta}" "~{reads_aligned_bam}" \
           | bcftools call \
           -P 0 -m --ploidy 1 \
           --threads $(nproc) \
           -Ov -o everything.vcf
 
         # mask all GT calls when less than 3 reads
-        cat everything.vcf | bcftools filter -e "FMT/DP<${min_coverage}" -S . > filtered.vcf
-        cat filtered.vcf | bcftools filter -i "MAC>0" > "${out_basename}.discordant.vcf"
+        cat everything.vcf | bcftools filter -e "FMT/DP<~{min_coverage}" -S . > filtered.vcf
+        cat filtered.vcf | bcftools filter -i "MAC>0" > "~{out_basename}.discordant.vcf"
 
         # tally outputs
         bcftools filter -i 'MAC=0' filtered.vcf | bcftools query -f '%POS\n' | wc -l | tee num_concordant
-        bcftools filter -i 'TYPE="snp"'  "${out_basename}.discordant.vcf" | bcftools query -f '%POS\n' | wc -l | tee num_discordant_snps
-        bcftools filter -i 'TYPE!="snp"' "${out_basename}.discordant.vcf" | bcftools query -f '%POS\n' | wc -l | tee num_discordant_indels
+        bcftools filter -i 'TYPE="snp"'  "~{out_basename}.discordant.vcf" | bcftools query -f '%POS\n' | wc -l | tee num_discordant_snps
+        bcftools filter -i 'TYPE!="snp"' "~{out_basename}.discordant.vcf" | bcftools query -f '%POS\n' | wc -l | tee num_discordant_indels
     }
 
     output {
-        File   discordant_sites_vcf = "${out_basename}.discordant.vcf"
+        File   discordant_sites_vcf = "~{out_basename}.discordant.vcf"
         Int    concordant_sites     = read_int("num_concordant")
         Int    discordant_snps      = read_int("num_discordant_snps")
         Int    discordant_indels    = read_int("num_discordant_indels")
@@ -771,7 +771,7 @@ task run_discordance {
     }
 
     runtime {
-        docker: "${docker}"
+        docker: docker
         memory: "3 GB"
         cpu: 2
         disks: "local-disk 100 HDD"
diff --git a/pipes/WDL/tasks/tasks_demux.wdl b/pipes/WDL/tasks/tasks_demux.wdl
index e2cbd5cae..ed392824a 100644
--- a/pipes/WDL/tasks/tasks_demux.wdl
+++ b/pipes/WDL/tasks/tasks_demux.wdl
@@ -361,7 +361,8 @@ task illumina_demux {
 
     cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
     cat /proc/loadavg | cut -f 3 -d ' ' > LOAD_15M
-    cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
+    set +o pipefail
+    { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
   >>>
 
   output {
diff --git a/pipes/WDL/tasks/tasks_nextstrain.wdl b/pipes/WDL/tasks/tasks_nextstrain.wdl
index 315087245..692f78cc4 100644
--- a/pipes/WDL/tasks/tasks_nextstrain.wdl
+++ b/pipes/WDL/tasks/tasks_nextstrain.wdl
@@ -151,7 +151,7 @@ task nextclade_many_samples {
         # gather runtime metrics
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
     >>>
     runtime {
         docker: docker
@@ -523,7 +523,7 @@ task nextstrain_build_subsample {
         cd ..
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
     >>>
     runtime {
         docker: docker
@@ -725,7 +725,7 @@ task filter_subsample_sequences {
         }
     }
     String out_fname = sub(sub(basename(sequences_fasta), ".vcf", ".filtered.vcf"), ".fasta$", ".filtered.fasta")
-    command {
+    command <<<
         set -e
         augur version > VERSION
 
@@ -764,8 +764,8 @@ task filter_subsample_sequences {
         grep "strains passed all filters" STDOUT | cut -f 1 -d ' ' > OUT_COUNT
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "15 GB"
@@ -858,7 +858,7 @@ task filter_sequences_to_list {
 
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
     >>>
     runtime {
         docker: docker
@@ -897,7 +897,7 @@ task mafft_one_chr {
         Int      mem_size = 500
         Int      cpus = 64
     }
-    command {
+    command <<<
         set -e
 
         # decompress sequences if necessary
@@ -947,8 +947,8 @@ task mafft_one_chr {
         # profiling and stats
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: mem_size + " GB"
@@ -983,7 +983,7 @@ task mafft_one_chr_chunked {
         Int      mem_size = 32
         Int      cpus = 96
     }
-    command {
+    command <<<
         set -e
 
         # write out ref
@@ -1053,8 +1053,8 @@ task mafft_one_chr_chunked {
         # profiling and stats
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: mem_size + " GB"
@@ -1087,7 +1087,7 @@ task augur_mafft_align {
 
         String  docker = "nextstrain/base:build-20211012T204409Z"
     }
-    command {
+    command <<<
         set -e
         augur version > VERSION
         augur align --sequences "~{sequences}" \
@@ -1100,8 +1100,8 @@ task augur_mafft_align {
             --nthreads auto
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "180 GB"
@@ -1163,7 +1163,7 @@ task augur_mask_sites {
         }
     }
     String out_fname = sub(sub(basename(sequences), ".vcf", ".masked.vcf"), ".fasta$", ".masked.fasta")
-    command {
+    command <<<
         set -e
         augur version > VERSION
         BEDFILE=~{select_first([mask_bed, "/dev/null"])}
@@ -1176,8 +1176,8 @@ task augur_mask_sites {
         fi
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "3 GB"
@@ -1219,7 +1219,7 @@ task draft_augur_tree {
         }
     }
     String out_basename = basename(basename(basename(msa_or_vcf, '.gz'), '.vcf'), '.fasta')
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur tree --alignment "~{msa_or_vcf}" \
@@ -1232,8 +1232,8 @@ task draft_augur_tree {
             --nthreads auto
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "32 GB"
@@ -1286,7 +1286,7 @@ task refine_augur_tree {
         }
     }
     String out_basename = basename(basename(basename(msa_or_vcf, '.gz'), '.vcf'), '.fasta')
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur refine \
@@ -1313,8 +1313,8 @@ task refine_augur_tree {
             ~{"--vcf-reference " + vcf_reference}
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "50 GB"
@@ -1350,7 +1350,7 @@ task ancestral_traits {
         String        docker = "nextstrain/base:build-20211012T204409Z"
     }
     String out_basename = basename(tree, '.nwk')
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur traits \
@@ -1363,8 +1363,8 @@ task ancestral_traits {
             ~{true="--confidence" false="" confidence}
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "32 GB"
@@ -1407,7 +1407,7 @@ task ancestral_tree {
         }
     }
     String out_basename = basename(basename(basename(msa_or_vcf, '.gz'), '.vcf'), '.fasta')
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur ancestral \
@@ -1423,8 +1423,8 @@ task ancestral_tree {
             ~{true="--infer-ambiguous" false="" infer_ambiguous}
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "50 GB"
@@ -1460,7 +1460,7 @@ task translate_augur_tree {
         String docker = "nextstrain/base:build-20211012T204409Z"
     }
     String out_basename = basename(tree, '.nwk')
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur translate --tree "~{tree}" \
@@ -1470,8 +1470,8 @@ task translate_augur_tree {
             ~{"--vcf-reference " + vcf_reference} \
             ~{"--genes " + genes} \
             --output-node-data ~{out_basename}_aa_muts.json
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "2 GB"
@@ -1515,7 +1515,7 @@ task tip_frequencies {
         String   docker = "nextstrain/base:build-20211012T204409Z"
         String   out_basename = basename(tree, '.nwk')
     }
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur frequencies \
@@ -1539,8 +1539,8 @@ task tip_frequencies {
 
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: select_first([machine_mem_gb, 30]) + " GB"
@@ -1573,7 +1573,7 @@ task assign_clades_to_nodes {
         String docker = "nextstrain/base:build-20211012T204409Z"
     }
     String out_basename = basename(basename(tree_nwk, ".nwk"), "_timetree")
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur clades \
@@ -1582,8 +1582,8 @@ task assign_clades_to_nodes {
         --reference "~{ref_fasta}" \
         --clades "~{clades_tsv}" \
         --output-node-data "~{out_basename}_clades.json"
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "2 GB"
@@ -1616,7 +1616,7 @@ task augur_import_beast {
         String  docker = "nextstrain/base:build-20211012T204409Z"
     }
     String tree_basename = basename(beast_mcc_tree, ".tree")
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur import beast \
@@ -1629,8 +1629,8 @@ task augur_import_beast {
             ~{"--tip-date-delimeter " + tip_date_delimiter}
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: select_first([machine_mem_gb, 3]) + " GB"
@@ -1674,7 +1674,7 @@ task export_auspice_json {
         String docker = "nextstrain/base:build-20211012T204409Z"
     }
     
-    command {
+    command <<<
         set -e -o pipefail
         augur version > VERSION
         touch exportargs
@@ -1728,8 +1728,9 @@ task export_auspice_json {
         touch "~{out_basename}_auspice_root-sequence.json"
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-    }
+        set +o pipefail
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "32 GB"
diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl
index 203393ee5..f8871b9aa 100644
--- a/pipes/WDL/tasks/tasks_reports.wdl
+++ b/pipes/WDL/tasks/tasks_reports.wdl
@@ -502,17 +502,18 @@ task compare_two_genomes {
     String docker = "quay.io/broadinstitute/viral-assemble:2.1.16.1"
   }
 
-  command {
+  command <<<
     set -ex -o pipefail
     assembly.py --version | tee VERSION
-    assembly.py alignment_summary "${genome_one}" "${genome_two}" --outfileName "${out_basename}.txt" --printCounts --loglevel=DEBUG
+    assembly.py alignment_summary "~{genome_one}" "~{genome_two}" --outfileName "~{out_basename}.txt" --printCounts --loglevel=DEBUG
     cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
     cat /proc/loadavg > CPU_LOAD
-    cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-  }
+    set +o pipefail
+    { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+  >>>
 
   output {
-    File   comparison_table = "${out_basename}.txt"
+    File   comparison_table = "~{out_basename}.txt"
     Int    max_ram_gb       = ceil(read_float("MEM_BYTES")/1000000000)
     Int    runtime_sec      = ceil(read_float("UPTIME_SEC"))
     String cpu_load         = read_string("CPU_LOAD")
@@ -522,7 +523,7 @@ task compare_two_genomes {
   runtime {
     memory: "3 GB"
     cpu: 2
-    docker: "${docker}"
+    docker: docker
     disks: "local-disk 50 HDD"
     dx_instance_type: "mem1_ssd1_v2_x2"
     preemptible: 1
diff --git a/pipes/WDL/tasks/tasks_utils.wdl b/pipes/WDL/tasks/tasks_utils.wdl
index 89b1a8996..881157855 100644
--- a/pipes/WDL/tasks/tasks_utils.wdl
+++ b/pipes/WDL/tasks/tasks_utils.wdl
@@ -35,6 +35,7 @@ task zcat {
         Int         cpus = 4
     }
     command <<<
+        set -e
         python3 <<CODE
         import os.path
         import gzip, lzma, bz2
@@ -97,7 +98,7 @@ task zcat {
         # gather runtime metrics
         cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
         cat /proc/loadavg > CPU_LOAD
-        cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
     >>>
     runtime {
         docker: "quay.io/broadinstitute/viral-core:2.1.33"