diff --git a/tasks/tasks_nextstrain.wdl b/tasks/tasks_nextstrain.wdl
index a833a2ee..a7a6c431 100644
--- a/tasks/tasks_nextstrain.wdl
+++ b/tasks/tasks_nextstrain.wdl
@@ -15,7 +15,7 @@ task nextclade_one_sample {
         String docker = "nextstrain/nextclade:1.7.0"
     }
     String basename = basename(genome_fasta, ".fasta")
-    command {
+    command <<<
         set -e
         apt-get update
         apt-get -y install python3
@@ -57,7 +57,7 @@ task nextclade_one_sample {
         grep ^clade transposed.tsv | cut -f 2 | grep -v clade > NEXTCLADE_CLADE
         grep ^aaSubstitutions transposed.tsv | cut -f 2 | grep -v aaSubstitutions > NEXTCLADE_AASUBS
         grep ^aaDeletions transposed.tsv | cut -f 2 | grep -v aaDeletions > NEXTCLADE_AADELS
-    }
+    >>>
     runtime {
         docker: docker
         memory: "3 GB"
@@ -147,7 +147,7 @@ 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
@@ -351,8 +351,7 @@ task derived_cols {
         awk '!a[$1]++' "~{basename}.derived_cols.tsv" > temp.tsv && mv temp.tsv "~{basename}.derived_cols.tsv"
 
         # convert to csv
-        tr '\t' ',' < "~{basename}.derived_cols.tsv" > "~{basename}.derived_cols.csv"
-        
+        csvformat --tabs "~{basename}.derived_cols.tsv" > "~{basename}.derived_cols.csv"
     >>>
     runtime {
         docker: docker
@@ -526,7 +525,7 @@ 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
@@ -555,11 +554,11 @@ task nextstrain_ncov_defaults {
         String nextstrain_ncov_repo_commit = "cf79e41d4178608bda4b084080f0ffff5b3da61c"
         String docker                      = "nextstrain/base:build-20220111T004537Z"
     }
-    command {
+    command <<<
         set -e
         wget -q "https://github.com/nextstrain/ncov/archive/~{nextstrain_ncov_repo_commit}.tar.gz"
         tar -xf "~{nextstrain_ncov_repo_commit}.tar.gz" --strip-components=1
-    }
+    >>>
     runtime {
         docker: docker
         memory: "1 GB"
@@ -635,7 +634,6 @@ task nextstrain_ncov_sanitize_gisaid_data {
     meta {
         description: "Sanitize data downloaded from GISAID for use in Nextstrain/augur. See: https://nextstrain.github.io/ncov/data-prep#curate-data-from-the-full-gisaid-database"
     }
-
     input {
         File sequences_gisaid_fasta
         File metadata_gisaid_tsv
@@ -645,7 +643,6 @@ task nextstrain_ncov_sanitize_gisaid_data {
         String nextstrain_ncov_repo_commit = "cf79e41d4178608bda4b084080f0ffff5b3da61c"
         String docker                      = "nextstrain/base:build-20220111T004537Z"
     }
-
     parameter_meta {
         sequences_gisaid_fasta: {
           description: "Multiple sequences downloaded from GISAID",
@@ -661,7 +658,7 @@ task nextstrain_ncov_sanitize_gisaid_data {
     }
 
     String out_basename = basename(basename(basename(basename(sequences_gisaid_fasta, '.xz'), '.gz'), '.tar'), '.fasta')
-    command {
+    command <<<
         set -e
         ncov_path_prefix="/nextstrain/ncov"
         wget -q "https://github.com/nextstrain/ncov/archive/~{nextstrain_ncov_repo_commit}.tar.gz"
@@ -679,7 +676,7 @@ task nextstrain_ncov_sanitize_gisaid_data {
         --rename-fields 'Virus name=strain' 'Accession ID=gisaid_epi_isl' 'Collection date=date' 'Clade=GISAID_clade' 'Pango lineage=pango_lineage' 'Host=host' 'Type=virus' 'Patient age=age' \
         ~{"--strip-prefixes=" + prefix_to_strip} \
         --output "~{out_basename}_metadata_sanitized_for_nextstrain.tsv.gz"
-    }
+    >>>
     runtime {
         docker: docker
         memory: "7 GB"
@@ -730,7 +727,7 @@ 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
 
@@ -769,8 +766,8 @@ 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"
@@ -863,7 +860,7 @@ 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
@@ -902,7 +899,7 @@ task mafft_one_chr {
         Int      mem_size = 500
         Int      cpus = 64
     }
-    command {
+    command <<<
         set -e
 
         # decompress sequences if necessary
@@ -952,8 +949,8 @@ 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"
@@ -988,7 +985,7 @@ task mafft_one_chr_chunked {
         Int      mem_size = 32
         Int      cpus = 96
     }
-    command {
+    command <<<
         set -e
 
         # write out ref
@@ -1058,8 +1055,8 @@ 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"
@@ -1092,7 +1089,7 @@ task augur_mafft_align {
 
         String  docker = "nextstrain/base:build-20220111T004537Z"
     }
-    command {
+    command <<<
         set -e
         augur version > VERSION
         augur align --sequences "~{sequences}" \
@@ -1105,8 +1102,8 @@ 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"
@@ -1132,10 +1129,10 @@ task snp_sites {
         String  docker = "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
     }
     String out_basename = basename(msa_fasta, ".fasta")
-    command {
+    command <<<
         snp-sites -V > VERSION
         snp-sites -v ~{true="" false="-c" allow_wildcard_bases} -o "~{out_basename}.vcf" "~{msa_fasta}"
-    }
+    >>>
     runtime {
         docker: docker
         memory: "31 GB"
@@ -1168,7 +1165,7 @@ 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"])}
@@ -1181,8 +1178,8 @@ 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"
@@ -1224,7 +1221,7 @@ 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}" \
@@ -1237,8 +1234,8 @@ 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"
@@ -1291,7 +1288,7 @@ 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 \
@@ -1318,8 +1315,8 @@ 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"
@@ -1355,7 +1352,7 @@ task ancestral_traits {
         String        docker = "nextstrain/base:build-20220111T004537Z"
     }
     String out_basename = basename(tree, '.nwk')
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur traits \
@@ -1368,8 +1365,8 @@ 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"
@@ -1412,7 +1409,7 @@ 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 \
@@ -1428,8 +1425,8 @@ 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"
@@ -1465,7 +1462,7 @@ task translate_augur_tree {
         String docker = "nextstrain/base:build-20220111T004537Z"
     }
     String out_basename = basename(tree, '.nwk')
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur translate --tree "~{tree}" \
@@ -1475,8 +1472,8 @@ 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"
@@ -1520,7 +1517,7 @@ task tip_frequencies {
         String   docker = "nextstrain/base:build-20220111T004537Z"
         String   out_basename = basename(tree, '.nwk')
     }
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur frequencies \
@@ -1544,8 +1541,8 @@ 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"
@@ -1578,7 +1575,7 @@ task assign_clades_to_nodes {
         String docker = "nextstrain/base:build-20220111T004537Z"
     }
     String out_basename = basename(basename(tree_nwk, ".nwk"), "_timetree")
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur clades \
@@ -1587,8 +1584,8 @@ 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"
@@ -1621,7 +1618,7 @@ task augur_import_beast {
         String  docker = "nextstrain/base:build-20220111T004537Z"
     }
     String tree_basename = basename(beast_mcc_tree, ".tree")
-    command {
+    command <<<
         set -e
         augur version > VERSION
         AUGUR_RECURSION_LIMIT=10000 augur import beast \
@@ -1634,8 +1631,8 @@ 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"
@@ -1679,7 +1676,7 @@ task export_auspice_json {
         String docker = "nextstrain/base:build-20220111T004537Z"
     }
     
-    command {
+    command <<<
         set -e -o pipefail
         augur version > VERSION
         touch exportargs
@@ -1733,8 +1730,8 @@ 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
-    }
+        { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+    >>>
     runtime {
         docker: docker
         memory: "32 GB"
@@ -1755,7 +1752,6 @@ task export_auspice_json {
 }
 
 task prep_augur_metadata {
-
   input {
     File      assembly
     String    collection_date
@@ -1766,15 +1762,13 @@ task prep_augur_metadata {
 
     String? iso_county=""
 
-
     String    docker_image = "quay.io/theiagen/utility:1.1"
     Int       mem_size_gb = 3
     Int       CPUs = 1
     Int       disk_size = 10
     Int       preemptible_tries = 0
   }
-
-  command {
+  command <<<
     # de-identified consensus/assembly sequence
     year=$(echo ${collection_date} | cut -f 1 -d '-')
 
@@ -1786,13 +1780,10 @@ task prep_augur_metadata {
     echo -e "\"$assembly_header\"\t\"ncov\"\t\"${collection_date}\"\t\"${iso_continent}\" \t\"${iso_country}\"\t\"${iso_state}\"\t\"${iso_county}\"\t"${pango_lineage}"" >> augur_metadata.tsv
 
     echo $(ls )
-
-  }
-
+  >>>
   output {
     File     augur_metadata = "augur_metadata.tsv"
   }
-
   runtime {
       docker:       docker_image
       memory:       "~{mem_size_gb} GB"
diff --git a/tasks/tasks_reports.wdl b/tasks/tasks_reports.wdl
index 40bc36fa..a3ef6a0f 100644
--- a/tasks/tasks_reports.wdl
+++ b/tasks/tasks_reports.wdl
@@ -338,7 +338,7 @@ task MultiQC {
   # get the basename in all wdl use the filename specified (sans ".html" extension, if specified)
   String report_filename = if (defined(file_name)) then basename(select_first([file_name]), ".html") else "multiqc"
 
-  command {
+  command <<<
       set -ex -o pipefail
 
       echo "${sep='\n' input_files}" > input-filenames.txt
@@ -378,7 +378,7 @@ task MultiQC {
       fi
 
       tar -c "${out_dir}/${report_filename}_data" | gzip -c > "${report_filename}_data.tar.gz"
-  }
+  >>>
 
   output {
       File multiqc_report            = "${out_dir}/${report_filename}.html"
@@ -399,13 +399,11 @@ task tsv_join {
   meta {
       description: "Perform a full left outer join on multiple TSV tables. Each input tsv must have a header row, and each must must contain the value of id_col in its header. Inputs may or may not be gzipped. Unix/Mac/Win line endings are tolerated on input, Unix line endings are emitted as output. Unicode text safe."
   }
-
   input {
     Array[File]+   input_tsvs
     String         id_col
     String         out_basename = "merged"
   }
-
   command <<<
     python3<<CODE
     import collections
@@ -449,11 +447,9 @@ task tsv_join {
         writer.writerows(out_row_by_id[row_id] for row_id in out_ids)
     CODE
   >>>
-
   output {
     File   out_tsv = "${out_basename}.tsv"
   }
-
   runtime {
     memory: "7 GB"
     cpu: 1
@@ -470,18 +466,15 @@ task tsv_stack {
     String         out_basename
     String         docker="quay.io/broadinstitute/viral-core:2.1.19"
   }
-
-  command {
+  command <<<
     csvstack -t --filenames \
       ${sep=' ' input_tsvs} \
       | tr , '\t' \
       > ${out_basename}.txt
-  }
-
+  >>>
   output {
     File   out_tsv = "${out_basename}.txt"
   }
-
   runtime {
     memory: "1 GB"
     cpu: 1
@@ -490,7 +483,6 @@ task tsv_stack {
     dx_instance_type: "mem1_ssd1_v2_x2"
     maxRetries: 3
   }
-
 }
 
 task compare_two_genomes {
@@ -501,16 +493,14 @@ 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 "${out_basename}.txt" --printCounts --loglevel=DEBUG
     cat /proc/uptime | cut -f 1 -d ' ' > UPTIME_SEC
     cat /proc/loadavg > CPU_LOAD
-    cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes > MEM_BYTES
-  }
-
+    { cat /sys/fs/cgroup/memory/memory.max_usage_in_bytes || echo 0; } > MEM_BYTES
+  >>>
   output {
     File   comparison_table = "${out_basename}.txt"
     Int    max_ram_gb = ceil(read_float("MEM_BYTES")/1000000000)
@@ -518,7 +508,6 @@ task compare_two_genomes {
     String cpu_load = read_string("CPU_LOAD")
     String viralngs_version = read_string("VERSION")
   }
-
   runtime {
     memory: "3 GB"
     cpu: 2
diff --git a/tasks/tasks_utils.wdl b/tasks/tasks_utils.wdl
index f5c80898..bca75031 100644
--- a/tasks/tasks_utils.wdl
+++ b/tasks/tasks_utils.wdl
@@ -118,7 +118,7 @@ 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"