A researcher here was trying to use Galaxy Picard sam2fastq tool to generate a single fastq file from a sam file that has a mix of paired and unpaired data. She was thinking the second input on the sheet might control this:

Do you want to output a fastq file per read group (two fastq files per read group if the group is paired) YesNo OUTPUT_PER_RG; default=False

But preliminary testing indicates there is no output scenario that includes both paired and unpaired data in the output (esp. as just one file). I just wanted to verify that this was the case, since the docs don't talk about this scenario? We're planning instead to write a little Galaxy tool that does what she gets accomplished on the command line:

samtools view -bS in.sam > out.bam bamtools convert -format fastq -in in.bam > out.fastq

which includes unpaired reads too. Thanks for feedback, d. Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada