Hi. I see an example here https://docs.galaxyproject.org/en/latest/dev/schema.html that && is used to separate two lines:
mkdir -p output_dir &&
python $__tool_directory__/extract_genomic_dna.py
However, when I used && in my xml, it doesn't work - it is not showing up on galaxy when I run run.sh unless I delete &&. So my question is - will this cause a problem ? (Galaxy doesn't give error when I don't add && but the result seems different from what I got from the command line) Is there something to fix in my lines below?
Also the reason I added 2>/dev/null is because bwa aln will print stdout to stderr and galaxy will throw the error message.
#if $seq.method == "singleEnd":
bwa aln -t $nThrds -n $MaxDiff -q $TrimQual ${Ref_fa}.fa $seq.input_query_fq 2>/dev/null > sai &&
bwa samse ${Ref_fa}.fa sai $seq.input_query_fq
#end if
> $output
