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allow custom placeholder for missing data in tsv_join task #227

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allow custom placeholder for missing data in tsv_join task #227

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2d62954
allow custom placeholder for missing data in tsv_join task
tomkinsc Mar 11, 2021
df439a6
fallback properly
tomkinsc Mar 11, 2021
7f27dd8
Merge branch 'master' into ct-tsv_join-default-placeholder
tomkinsc Mar 30, 2021
33199ac
Merge branch 'master' into ct-tsv_join-default-placeholder
tomkinsc Jun 14, 2021
3f222b8
move changed placeholder code to reflect upstream move of tsv_join fr…
tomkinsc Jun 14, 2021
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5 changes: 3 additions & 2 deletions pipes/WDL/tasks/tasks_utils.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,7 @@ task tsv_join {
Array[File]+ input_tsvs
String id_col
String out_basename = "merged"
String placeholder_for_missing = ""
}

command <<<
Expand Down Expand Up @@ -210,8 +211,8 @@ task tsv_join {
row_out = out_row_by_id.get(row_id, {})
for h in header:
# prefer non-empty values from earlier files in in_tsvs, populate from subsequent files only if missing
if not row_out.get(h):
row_out[h] = row.get(h, '')
if row_out.get(h, '~{placeholder_for_missing}') == '~{placeholder_for_missing}':
row_out[h] = row.get(h, '~{placeholder_for_missing}')
out_row_by_id[row_id] = row_out
out_ids.append(row_id)
out_ids = list(collections.OrderedDict(((i,0) for i in out_ids)).keys())
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7 changes: 4 additions & 3 deletions pipes/WDL/workflows/sarscov2_nextstrain.wdl
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Expand Up @@ -78,9 +78,10 @@ workflow sarscov2_nextstrain {
if(length(sample_metadata_tsvs)>1) {
call utils.tsv_join {
input:
input_tsvs = sample_metadata_tsvs,
id_col = 'strain',
out_basename = "metadata-merged"
input_tsvs = sample_metadata_tsvs,
id_col = 'strain',
out_basename = "metadata-merged"
placeholder_for_missing = "?"
}
}
call nextstrain.derived_cols {
Expand Down