Recipe for Expansaion Hunter, fixes #442 #463
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| - pexpansionhunter | ||
| data_type: SCALAR | ||
| exists_check: directory | ||
| mandatory: no |
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Is it not mandatory to supply "expansionhunter_repeat_specs_dir" to run with expansionhunter?
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You need to have the repeat spec files for running the program. I'm trying to set the repeat spec directory to the one supplied with the program if you haven't supplied the path in the config
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| sub analysis_expansionhunter { | ||
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| ## Function : Call expansions of STR using Expansion Hunter |
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STR -> Short tandem repeats (STR)
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| my ($arg_href) = @_; | ||
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| ## Default(s) |
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Move block under ## Flatten argument(s) to comply with latest template
| ## Creates program directories (info & programData & programScript), program script filenames and writes sbatch header | ||
| my ( $file_path, $program_info_path ) = setup_script( | ||
| { | ||
| active_parameter_href => $active_parameter_href, |
| } | ||
| ); | ||
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| #Used downstream |
| { | ||
| parameter_href => $parameter_href, | ||
| suffix_key => q{variant_file_suffix}, | ||
| job_id_chain => $job_id_chain, |
| ); | ||
| say {$FILEHANDLE} q{wait} . $NEWLINE; | ||
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| ## Rename the bam file index file so that Expansion Hunter can find it |
| ); | ||
| } | ||
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| if ( not -d $repeat_specs_dir_path ) { |
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This is to late since MIP will have launched all programs upstream already. This must be checked before launching to SLURM. We should always check everything before that and fail if required. Would be nice to add to: set_custom_default_to_active_parameter in MAIN/Analyse.pm
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True! Will move the check
| { | ||
| FILEHANDLE => $FILEHANDLE, | ||
| infile_path => $file_path_prefix . $infile_suffix, | ||
| json_outfile_path => $outfile_path_prefix . q{.json}, |
| return; | ||
| } | ||
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| sub _get_default_repeat_specs_dir_path { |
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Move this to MAIN/Analyse.pm set_custom_default_to_active_parameter part for rare_disease (only)
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Awesome! |
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