Workflow: AltAnalyze Prepare Genome

Fetched 2023-09-14 02:52:18 GMT

Devel version of AltAnalyze Prepare Genome ========================================== hg38 is not supported. Use hardcoded EnsMart72 until AltAnalyze starts support more recent Ensembl releases.

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Inputs

ID Type Title Doc
alias String Experiment short name/Alias
genome Genome type

Genome type, such as mm10, hg19, hg38, etc

Steps

ID Runs Label Doc
altanalyze_prepare_genome
../tools/altanalyze-prepare-genome.cwl (CommandLineTool)

Downloads data from the Ensembl Database based on the selected genome. Output folder name will be always equal to ENSEMBL_VERSION__SPECIES.

AltAnalyze has problems downloading EnsMart69 and EnsMart78, so only hg19 genome is currently supported.

Outputs

ID Type Label Doc
genome_data Directory AltAnalyze genome data

Pre-downloaded Ensembl database for the specific genome

altanalyze_prepare_genome_stderr_log File stderr log generated by altanalyze prepare genome

stderr log generated by altanalyze prepare genome

altanalyze_prepare_genome_stdout_log File stdout log generated by altanalyze prepare genome

stdout log generated by altanalyze prepare genome

Permalink: https://w3id.org/cwl/view/git/954bb2f213d97dfef1cddaf9e830169a92ad0c6b/workflows/altanalyze-prepare-genome.cwl