Bismark - Bug in Bismark Pretty Report ?

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Bismark - Bug in Bismark Pretty Report ?

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
Tool Standard Error: 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.
additional_reports
Submit the corresponding Bismark deduplication report 197: Bismark Deduplicate on data 133: deduplication report
Submit the corresponding Bismark splitting report 189: Bismark Meth. Extractor on data 60 and data 133: Splitting Report
Submit the corresponding Bismark M-bias report 190: Bismark Meth. Extractor on data 60 and data 133: Mbias Report
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

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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Bismark_Pretty_Report_on_data_190,_data_189,_and_others__Download_pretty_html_report_html.html (3M) Download Attachment