How to set a multiqc outpath

Question

[michael.flower.14]

I'm using multiqc to produce a single QC report for my fastq files. However, I can't work out how to use the -o and -outdir flags to pipe the output file to a directory of my choosing. Any help would be great, thanks. At the moment it just outputs the file into my home directory.

conda activate bioinfo
export LC_ALL=en_GB.UTF-8
export LANG=en_GB.UTF-8
conda update networks
fastqc --extract ~/bin/biostarhb/ch2ot_S7_L001_R1_001.fastq.gz ~/bin/biostarhb/ch2ot_S7_L001_R2_001.fastq.gz
multiqc ~/bin/biostarhb/ch2ot_S7_L001_R1_001_fastqc/ ~/bin/biostarhb/ch2ot_S7_L001_R2_001_fastqc/

Answer 1

[GenoMax]

You can simply point multiqc to folder of fastqc reports and set the output directory to whatever you want

multiqc /dir_with_fastqc_reports -o directory_you_want

If your reports are in different directories then you can do

multiqc ~/bin/biostarhb/ch2ot_S7_L001_R1_001_fastqc/ ~/bin/biostarhb/ch2ot_S7_L001_R2_001_fastqc/ -o dir_you_want_for_output

[michael.flower.14]

Perfect thanks, that worked well