trimmed output not as documented

[gpalidwor]

Description of the bug

Using smrnaseq v2.0.0, I see this with the example minimal dataset output, it's also the case in the AWS output.

The documentation says trimming will go into results/trim_galore, but it goes into results/trimmed. As well the trimmed directory does not contain the trimmed fastq.gz output as documented.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[apeltzer]

Looking at this here -

smrnaseq/conf/modules.config

Line 111 in 4278785

pattern: "*.txt"

I think the *.{txt,fastq.gz} pattern should be enough to fix this . Will do this in dev now.