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mobinasri / flagger

Evaluating genome assemblies
MIT License
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end to end wdl run requires more parameters than specified in readme #40

Closed Dmitry-Antipov closed 1 week ago

Dmitry-Antipov commented 2 weeks ago

Hi I was trying to run hmm_flagger_end_to_end_with_mapping.wdl the way described in readme.

After modifying inputs.json, setting mandatory parameters: sampleName, suffixForFlagger, suffixForMapping, hap1AssemblyFasta, hap2AssemblyFasta, readFiles, presetForMapping and removing unspecified parameters (they will be set to default values), users can run the command below:

However pipeline failed requiring non-listed alphaTsv paramater: Required workflow input 'HMMFlaggerEndToEndWithMapping.alphaTsv' not specified

How should I specify this file? There's alpha_optimum_trunc_exp_gaussian_w_4000_n_50.tsv in flagger repo - is it just a test file or real parameters file that should be used by default?

mobinasri commented 1 week ago

Hi @Dmitry-Antipov Thanks for pointing this. Please use this file https://raw.githubusercontent.com/mobinasri/flagger/main/programs/config/alpha_optimum_trunc_exp_gaussian_w_4000_n_50.tsv I added this to README as well.

Dmitry-Antipov commented 1 week ago

Thank you for the clarification!