Bismark - Bug in Bismark Pretty Report ?

> Uha, this looks like a upstream bug, not sure how this can be Galaxy
> related.
>
> Is this still a problem?
>
> Cheers,
> Bjoern
>
> Am 08.03.19 um 09:23 schrieb Previti:
>> Dear Galaxy Community,
>>
>> I just recently started testing the Bismark methylation tools,
>> everything works fine until I try to make a "pretty report".
>> Some information is not included in the report, instead you see
>> placeholders
>> I attached the output I  get and shown below are the job parameters.
>> Does anybody know where to fix this?
>>
>> Best regards,
>> Christopher
>>
>>
>>     Bismark Pretty Report
>>
>>
>>       Dataset Information
>>
>> Number:     198
>> Name:     Bismark Pretty Report on data 190, data 189, and others:
>> Download pretty html report
>> Created:     Thu 07 Mar 2019 03:24:40 PM (UTC)
>> Filesize:     2.7 MB
>> Dbkey:     ?
>> Format:     html
>>
>>
>>       Job Information
>>
>> Galaxy Tool ID:
>> toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0
>> Galaxy Tool Version:     0.20.0
>> Tool Version:    
>> Tool Standard Output:     stdout
>> <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stdout>
>> Tool Standard Error:     stderr
>> <http://dkfzgalaxy/datasets/971c2f882eb14ac3/stderr>
>> Tool Exit Code:     0
>> History Content API ID:     971c2f882eb14ac3 (41433)
>> Job API ID:     58816697357e736f (22051)
>> History API ID:     5fccce9c1b3793da (807)
>> UUID:     45bedd12-6ce5-4d63-a1e2-e05883b0c356
>> Full Path:     /opt/galaxy/galaxy/database/files/038/dataset_38737.dat
>>
>>
>>       Tool Parameters
>>
>> Input Parameter     Value     Note for rerun
>> Submit a Bismark mapping report     191: Bismark Meth. Extractor on
>> data 60 and data 133: Genome-wide methylation report.
>> <http://dkfzgalaxy/datasets/c53067deacfc4f28/show_params>    
>> additional_reports    
>> Submit the corresponding Bismark deduplication report     197:
>> Bismark Deduplicate on data 133: deduplication report
>> <http://dkfzgalaxy/datasets/622377f5e70addd2/show_params>    
>> Submit the corresponding Bismark splitting report     189: Bismark
>> Meth. Extractor on data 60 and data 133: Splitting Report
>> <http://dkfzgalaxy/datasets/aa40ffd063a4645f/show_params>    
>> Submit the corresponding Bismark M-bias report     190: Bismark Meth.
>> Extractor on data 60 and data 133: Mbias Report
>> <http://dkfzgalaxy/datasets/47db6b20871008b9/show_params>    
>> Submit the corresponding Bismark nucleotide report    
>>     
>> Create a separate logfile, otherwise logs are added to the dataset
>> info.     False    
>>
>>
>>       Inheritance Chain
>>
>> Bismark Pretty Report on data 190, data 189, and others: Download
>> pretty html report
>>
>>
>>       Command Line
>>
>> python
>> '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/bismark/7bffcb6fc81d/bismark/bismark2report_wrapper.py' 
>> --alignment_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38715.dat' 
>> --dedup_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38736.dat'
>> --splitting_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38713.dat'
>> --mbias_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38714.dat' 
>> --output_html_report
>> '/opt/galaxy/galaxy/database/files/038/dataset_38737.dat'
>>
>>
>>       Job Metrics
>>
>>
>>         core
>>
>> Cores Allocated     8
>> Job End Time     2019-03-07 16:49:58
>> Job Runtime (Wall Clock)     25 minutes
>> Job Start Time     2019-03-07 16:24:43
>> Memory Allocated (MB)     510000
>>
>>
>>       Job Dependencies
>>
>> Dependency     Dependency Type     Version
>> bismark     conda     0.20.0
>>
>>
>>
>> -- 
>> *Dr. Christopher Previti*
>> Genomics and Proteomics Core Facility
>> High Throughput Sequencing (W190)
>> Bioinformatician
>>
>> German Cancer Research Center (DKFZ)
>> Foundation under Public Law
>> Im Neuenheimer Feld 580
>> 69120 Heidelberg
>> Germany
>> Room: B2.102 (INF580/TP3)
>> Phone: +49 6221 42-4661
>>
>> [hidden email] <http://www.dkfz.de/>
>> www.dkfz.de <http://www.dkfz.de/>
>>
>> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
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>>
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