If fastq files are name filename.fq.gz (instead of filename.fastq.gz) then trim_galore rule fails, because the functions that determine new file names for renaming (via mv) are hardcoded to replace 'fastq.gz' with '_trimmed.fastq.gz'. However, trim_galore will only insert the '_trimmed' part into the name and leave the file ending intact.
If fastq files are name filename.fq.gz (instead of filename.fastq.gz) then trim_galore rule fails, because the functions that determine new file names for renaming (via mv) are hardcoded to replace 'fastq.gz' with '_trimmed.fastq.gz'. However, trim_galore will only insert the '_trimmed' part into the name and leave the file ending intact.