Question: using SamToFastq 1.136.0 in Galaxy workflows
gravatar for shtatland
2.1 years ago by
shtatland0 wrote:


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 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

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!


tools picard workflows • 734 views
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by shtatland0

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

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson25k
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