bio-pipengine 0.9.1 → 0.9.2
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/lib/bio/pipengine.rb +12 -0
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: eb14c6fee1f60a6e21db6cad2b1d72ebed17e526
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4
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+
data.tar.gz: 4468852a5675dc250bcc9bec9cd255246721d50a
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 988fe20d0bddb1354b1f240c9d321b8029fa3303ee70d6c8b0de92a42595b4f4761956fa36b1c62edc82647437949f072583ce61a300d4251a8a941829433da4
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|
7
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+
data.tar.gz: b937716016a25772fd8db8373d3383d4e19899847c74a1b7d67aa97c7084388a31e55de63554d41794e33b2619782ced9de8e414af45bca3d224bba531ae239a
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data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.9.
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1
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+
0.9.2
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data/lib/bio/pipengine.rb
CHANGED
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@@ -11,6 +11,18 @@ module Bio
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11
11
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# reading the yaml files
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12
12
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pipeline = YAML.load ERB.new(File.read(options[:pipeline])).result(binding)
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13
13
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samples_file = load_samples_file options[:samples_file]
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14
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+
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15
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+
# make sure all sample names are always Strings
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16
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+
converted_samples_list = {}
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17
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+
samples_file["samples"].each_key do |sample|
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18
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+
if samples_file["samples"][sample].kind_of? Hash # it's a group of samples
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|
19
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+
converted_samples_list[sample.to_s] = Hash[samples_file["samples"][sample].map{ |k, v| [k.to_s, v] }]
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|
20
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+
else
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|
21
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+
converted_samples_list[sample.to_s] = samples_file["samples"][sample]
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|
22
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+
end
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23
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+
end
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24
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+
samples_file["samples"] = converted_samples_list # replacing original samples hash with the converted one
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25
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+
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14
26
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# pre-running checks
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15
27
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check_steps(options[:steps],pipeline)
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16
28
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check_samples(options[:samples],samples_file) if options[:samples]
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