How to properly specify a basename?

[jolespin]

(trim-galore_env) -bash-4.2$ trim_galore  -j 8 --basename Fastq/trimmed/${ID}/trimmed Fastq/raw/${ID}_R1_001.fastq.gz Fastq/raw/${ID}_R2_001.fastq.gz
Using an excessive number of cores has a diminishing return! It is recommended not to exceed 8 cores per trimming process (you asked for 8 cores). Please consider re-specifying
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 1.18
Could not detect version of Python used by Cutadapt from the first line of Cutadapt (but found this: >>>#!/bin/sh<<<)
Letting the (modified) Cutadapt deal with the Python version instead
pigz 2.6
Parallel gzip (pigz) detected. Proceeding with multicore (de)compression using 8 cores

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Using user-specified basename (>>Fastq/trimmed/0978C02A_AE_CSF_CD3PCD4P_Bch2_PLT4_1Cell_A10_S82/trimmed<<) instead of deriving the filename from the input file(s)
Please make sure the name specified with --basename does not contain file path information! (Fastq/trimmed/0978C02A_AE_CSF_CD3PCD4P_Bch2_PLT4_1Cell_A10_S82/trimmed) at /usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/trim-galore_env/bin/trim_galore line 2944.

I'm trying to get the following directory structure:

Fastq/trimmed/${ID}/trimmed_1.fastq.gz Fastq/trimmed/${ID}/trimmed_2.fastq.gz

or similar.

How can I specify a basename properly?

[FelixKrueger]

The parameter --basename allows you to specify a basename for the output files instead of deriving the name from the input files, for example --basename my_favouriteID. You could specify the output directory separately with -o:

-o/--output_dir <DIR>   If specified all output will be written to this directory instead of the current
                        directory. If the directory doesn't exist it will be created for you.

So for example: --basename my_favouriteID -o Fastq/trimmed/my_favouriteID/.

The output files within that directory will still get renamed according to standard Trim Galore naming conventions (i.e. my_favouriteID_R1_trimming_report.txt,...,my_favouriteID_R1_val_1.fq.gz,my_favouriteID_R2_val_2.fq.gz etc., but you can of you course rename the files once the run has finished.

[jolespin]

Thanks, that solved the issue.