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fix: fixed include flag KeyError #452

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merged 3 commits into from
Jan 20, 2022
Merged

fix: fixed include flag KeyError #452

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af00c9e
Fixed include flag KeyError
AKBrueggemann Jan 19, 2022
bd75b7f
Deleted else
AKBrueggemann Jan 19, 2022
36994c4
Merge branch 'master' into include-flag-fix
AKBrueggemann Jan 19, 2022
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19 changes: 15 additions & 4 deletions workflow/rules/common.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -1272,10 +1272,21 @@ def get_include_flag(sample):


def get_include_flag_for_date(wildcards):
return [
get_include_flag(sample)
for sample in get_assemblies_for_submission(wildcards, "accepted samples")
]
if len(get_samples_for_date(wildcards.date)) == len(
get_assemblies_for_submission(wildcards, "accepted samples")
):
return [
get_include_flag(sample) for sample in get_samples_for_date(wildcards.date)
]
else:
allsamplelist = []
for sample in get_samples_for_date(wildcards.date):
for sample_path in get_assemblies_for_submission(
wildcards, "accepted samples"
):
if sample in sample_path:
allsamplelist.append(sample)
return [get_include_flag(sample) for sample in allsamplelist]


def get_artic_primer(wildcards):
Expand Down