Copy SDRF functionality to output dir #22
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pcm32
commented
Feb 22, 2021
| my ( $investigation, $output_dir, $idf_abs_path ) = @_; | ||
| foreach my $sdrf ( @{ $investigation->get_sdrfs() } ) { | ||
| my $filename = $sdrf->get_uri()->file(); | ||
| if( !File::Spec->file_name_is_absolute( $filename ) ) { |
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This mostly assumes that SDRFs are in the same directory as the IDF, which is sound for Atlas, but this is not very defensive for more complex cases.
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Currently the condensed_sdrf script has a functionality to copy the IDF to the output directory, this gives the functionality to also copy the SDRF. This is needed to expose the SDRF files of baseline studies for meta-analysis.