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set AUGUR_RECURSION_LIMIT=10000 for augur commands #87

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May 27, 2020
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set AUGUR_RECURSION_LIMIT=10000 for augur commands #87

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18 changes: 9 additions & 9 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,7 @@ task draft_augur_tree {
}
command {
augur version > VERSION
augur tree --alignment ~{aligned_fasta} \
AUGUR_RECURSION_LIMIT=10000 augur tree --alignment ~{aligned_fasta} \
--output ~{basename}_raw_tree.nwk \
--method ~{default="iqtree" method} \
--substitution-model ~{default="GTR" substitution_model} \
Expand Down Expand Up @@ -254,7 +254,7 @@ task refine_augur_tree {
}
command {
augur version > VERSION
augur refine \
AUGUR_RECURSION_LIMIT=10000 augur refine \
--tree ~{raw_tree} \
--alignment ~{aligned_fasta} \
--metadata ~{metadata} \
Expand Down Expand Up @@ -311,7 +311,7 @@ task ancestral_traits {
}
command {
augur version > VERSION
augur traits \
AUGUR_RECURSION_LIMIT=10000 augur traits \
--tree ~{tree} \
--metadata ~{metadata} \
--columns ~{sep=" " columns} \
Expand Down Expand Up @@ -354,7 +354,7 @@ task ancestral_tree {
}
command {
augur version > VERSION
augur ancestral \
AUGUR_RECURSION_LIMIT=10000 augur ancestral \
--tree ~{refined_tree} \
--alignment ~{aligned_fasta} \
--output-node-data ~{basename}_nt_muts.json \
Expand Down Expand Up @@ -400,7 +400,7 @@ task translate_augur_tree {
}
command {
augur version > VERSION
augur translate --tree ~{refined_tree} \
AUGUR_RECURSION_LIMIT=10000 augur translate --tree ~{refined_tree} \
--ancestral-sequences ~{nt_muts} \
--reference-sequence ~{genbank_gb} \
~{"--vcf-reference-output " + vcf_reference_output} \
Expand Down Expand Up @@ -438,7 +438,7 @@ task assign_clades_to_nodes {
String out_basename = basename(basename(tree_nwk, ".nwk"), "_refined_tree")
command {
augur version > VERSION
augur clades \
AUGUR_RECURSION_LIMIT=10000 augur clades \
--tree ~{tree_nwk} \
--mutations ~{nt_muts_json} ~{aa_muts_json} \
--reference ~{ref_fasta} \
Expand Down Expand Up @@ -477,7 +477,7 @@ task augur_import_beast {
String tree_basename = basename(beast_mcc_tree, ".tree")
command {
augur version > VERSION
augur import beast \
AUGUR_RECURSION_LIMIT=10000 augur import beast \
--mcc "~{beast_mcc_tree}" \
--output-tree "~{tree_basename}.nwk" \
--output-node-data "~{tree_basename}.json" \
Expand Down Expand Up @@ -560,14 +560,14 @@ task export_auspice_json {
fi
cat $VALS >> exportargs

cat exportargs | tr '\n' '\0' | xargs -0 -t augur export v2 \
(export AUGUR_RECURSION_LIMIT=10000; cat exportargs | tr '\n' '\0' | xargs -0 -t augur export v2 \
--tree ~{tree} \
~{"--metadata " + sample_metadata} \
--auspice-config ~{auspice_config} \
~{"--lat-longs " + lat_longs_tsv} \
~{"--colors " + colors_tsv} \
~{"--description_md " + description_md} \
--output ~{out_basename}_auspice.json
--output ~{out_basename}_auspice.json)
}
runtime {
docker: docker
Expand Down