How to use the input freebayes "input_bams" to rename output

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How to use the input freebayes "input_bams" to rename output

Charles Girardot
Hi all,

I am a big fan of dataset renaming in my workflows, it helps a lot when you process tons of samples in parallel.

I have integrated FreeBayes in a workflow but renaming the output to “#{ input_bams }.vcf” fails.

I remember that when the input is a list, one needs to use some weird formulas, for example in the tool “Filter BAM datasets on a variety of attributes (Galaxy Tool Version 0.0.1)” that also defines a “input_bams", we could solve the issue with :

#{input_bams_0.input_bam}

So I mimicked this and tried #{input_bams_0.input_bam} , #{input_bams_0.input} and #{input_bams_0.bam} without success.

Does anyone has an idea what the correct spelling is for Freebayes ? I am sorry Jelle (our galaxy admin) is away this week  so I can’t tell you our server version but it is ~2 years old.

Thanks

Charles

=====================================
Charles Girardot
Head of Genome Biology Computational Support (GBCS)
and Senior Bioinformatician in the Furlong Lab
European Molecular Biology Laboratory
Tel: +49 6221 387 -8585
Fax: +49-(0)6221-387-8166
Email: [hidden email]
Web : http://gbcs.embl.de
Room V205
Meyerhofstraße 1,
69117 Heidelberg, Germany
=====================================


















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