bio-pipengine 0.9.1 → 0.9.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: eb14c6fee1f60a6e21db6cad2b1d72ebed17e526
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data.tar.gz: 4468852a5675dc250bcc9bec9cd255246721d50a
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SHA512:
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metadata.gz:
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data.tar.gz:
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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
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@@ -1 +1 @@
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1
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-
0.9.
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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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# reading the yaml files
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pipeline = YAML.load ERB.new(File.read(options[:pipeline])).result(binding)
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samples_file = load_samples_file options[:samples_file]
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# make sure all sample names are always Strings
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converted_samples_list = {}
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samples_file["samples"].each_key do |sample|
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if samples_file["samples"][sample].kind_of? Hash # it's a group of samples
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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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else
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converted_samples_list[sample.to_s] = samples_file["samples"][sample]
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end
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end
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samples_file["samples"] = converted_samples_list # replacing original samples hash with the converted one
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# pre-running checks
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check_steps(options[:steps],pipeline)
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check_samples(options[:samples],samples_file) if options[:samples]
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