Comments (4)
For the archive; to answer my own question:
after 2nd thought the solution was quite simple: before calling fastp
I only had to add a command to create a new directory:
mkdir -p $PWD/fastp_out/${fn}
That was all....
from fastp.
But actually this can be done with --json <dir/fastp.json> --html <dir/fastp.html>.
fastp will throw an error and quit immediately if you specify a existing folder name directly.
from fastp.
Yes yes of course, it was just an idea!
By default names were ok for me so I just try to give a directory to these 2 options and it did not work.
Thanks for your answer!
from fastp.
Likely a stupid question, but since I am struggling with something similar:
How to generate a report if I am using for <dir>
a character string that is composed of a directory name + fastq name? Thus e.g. 'samplenumber/fastqname'?
My file setup:
workingdir
seqdata
- sample1
--file1.fq.gz
- sample 2
--file2.fq.gz
pfast_out
In the working directory I am executing fastp
in a loop using:
#!/bin/bash
find $PWD/seqdata \( -name '*.fq.gz' -or -name '*.fq' \) -print0 | while read -d $'\0' fn
do
echo "Processing sample ${fn}"
fastp -i ${fn} -p -w 4 --json $PWD/pfast_out/${fn}/fastp.json --html $PWD/pfast_out/${fn}/fastp.html
done
The directory pfast_out
(in workingdir) is created by me before starting pfast
, but the *.json and *.html files are not generated??
Output names are: /workingdir/pfast_out/seqdata/sample1/file1.fq.gz/fastp.json, etc.
I think that since the sub-directory in bold doesn't exists when the files have to be written, the*.json and *.html files are not generated...
How to achieve this?
Thanks for any suggestions!
from fastp.
Related Issues (20)
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from fastp.