bio-fastqc 0.10.6 → 0.10.7
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/dockerfile/Dockerfile +1 -1
- data/lib/bio/fastqc/cli.rb +12 -2
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 3aa1e38f87a09d7211972e5ef8bde5717423b659346beca5eaea315918b64f6c
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4
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data.tar.gz: f601d5b3826e32eaf6a60f528ceac58f77745201a5856d9afdc41741b8659d1f
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: c96d2295b2d1628232411749be52a90dc461619b47e2b0f43458dd8b3149071883dbd7f9c95e5c5b783708f70d31c8b3d94bd1940e1e1207365823def32ad581
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7
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data.tar.gz: 5e0ba4dc8138e89819e0bb612a1ac3d5381e3a54e3b882176cc60b35043c0842e612fed929524d0177b61f4e25a7ad4c9010abd4a1f2b50fd4184eca203cc08c
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data/VERSION
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@@ -1 +1 @@
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1
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0.10.
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1
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0.10.7
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data/dockerfile/Dockerfile
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@@ -1,2 +1,2 @@
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FROM ruby:2.5.0-slim
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RUN gem install bio-fastqc -v 0.10.
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RUN gem install bio-fastqc -v 0.10.7
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data/lib/bio/fastqc/cli.rb
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@@ -6,13 +6,23 @@ require 'json'
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module Bio
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module FastQC
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class CLI < Thor
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desc "parse [--format format] [
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desc "parse [--format format] [--outdir output directory] [filepath, ..]", "parse fastqc data in directory or zipfile. output format: json, json-ld, turtle, or tsv"
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option :format, :default => "json"
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option :output, :default => nil
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def parse(*files)
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files.each do |file|
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data = Data.read(file)
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summary = Parser.new(data).summary
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out = Converter.new(summary).convert_to(options[:format])
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outdir_path = options[:outdir]
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if outdir_path && File.directory?(outdir_path)
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filename_org = File.basename(summary[:filename])
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fpath = File.join(outdir_path, filename_org + "." + options[:format])
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open(fpath, "w"){|f| f.puts(out) }
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else
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puts out
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end
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end
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end
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end
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