Treeval pipeline usage has a mistake

[Surbhigrewal]

Description of the bug

In https://pipelines.tol.sanger.ac.uk/treeval/dev/usage

under Longread data preparation > FASTQ -> FASTA
there is a code

mkdir fasta
cd fastq
for i in *fq; do
echo $i
j=${i%.fq}
echo $j
seqtk seq -a $i > ../fasta/${j}.fasta
done

But in line 7 on the website there is "& gt;" which should be ">" (like here).

I had to put a space between & and gt here so that github doesn't automatically convert it to >.

And then just below that in FASTA -> FASTA.GZ
this line below

for i in .fasta; do

should be

cd fasta
for i in *.fasta; do

For those that don't have coding background (like me) this might take hours to figure out why the code is not working and debug.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[DLBPointon]

Hi @Surbhigrewal

Thanks for the issue.
This may be an issue with the pipeline's website itself in how it renders some symbols. As you can see here: https://github.com/sanger-tol/treeval/blob/main/docs/usage.md the > are as we would expect e.g. showing a >. I'll talk to the maintainer and see if we can correct that at all or at least add a note.

The rest are completely fair points. There are some errors; we are approaching a Version 1.2 release, so I will make sure we do a thorough check of the documents. A chunk of it needs rewriting anyway!

Thanks for getting in touch!