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Question: using SamToFastq 1.136.0 in Galaxy workflows
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gravatar for shtatland
2.1 years ago by
shtatland • 0
shtatland • 0 wrote:

Hello,

How can I connect in the workflow SamToFastq and Bowtie2 tools in Galaxy? I am trying to convert (filtered) bam to 2 paired end fastq files and map them with bowtie. Apparently, the current version of SamToFastq is missing the fastq outputs in the user interface. It only has report (txt) output. I tested this on a local Galaxy instance and on https://usegalaxy.org. The tool versions are: SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq (Galaxy Version 1.136.0) Bowtie2 - map reads against reference genome (Galaxy Version 2.2.6.2)

Note that an older version of the same tool does not have this issue and can be connected with the noodle (tested on local Galaxy instance): SAM to FASTQ creates a FASTQ file (Galaxy Version 1.56.1)

Thank you!

Timur
tools picard workflows • 734 views
ADD COMMENT • link •
modified 2.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by shtatland • 0

This looks like a bug. Under review, feedback soon. Thanks for reporting the issue so clearly. Jen, Galaxy team

ADD REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for Jennifer Hillman Jackson
2.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I just retested and the issue is still problematic. I have opened a ticket for the development team to review/fix. Please follow progress here: https://github.com/galaxyproject/tools-devteam/issues/414

Thanks for reporting the problem! Jen, Galaxy team
ADD COMMENT • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k
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