Hi Daniel I ran the pipeline with ` user orfs faa` and ` use nf-core #metatdenovo

Hi Daniel, I ran the pipeline with `--user-orfs-f...

Mehrdad Jaberi

05/13/2025, 4:40 PM

Hi Daniel, I ran the pipeline with

--user-orfs-faa

and

--user-orfs-gff

and mistakenly defined

--orf-caller

. I see in the working directory, the

.command.sh

for the process

NFCORE_METATDENOVO:METATDENOVO:KOFAMSCAN:KOFAMSCAN_SCAN

used the correct input:

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exec_annotation \
    --profile profiles \
    --ko-list ko_list \
    --format detail-tsv \
    --cpu 6 \
    XXXXX.okay.aa \
    -o kofamscan_output.tsv

but in the results directory the naming is:

Copy code

results/kofamscan/sample_XXX.transdecoder.kofamscan_output.tsv.gz

I guess it is a naming issue?? I mean "transdecoder" has nothing to do with this output! right

Daniel Lundin

05/14/2025, 4:49 AM

Did you set

--orf-caller

transdecoder

? I'm not sure what would happen in this case, was

transdecoder

invoked?

Mehrdad Jaberi

05/14/2025, 8:33 AM

yes as mentioned I forgot to unset

orf-caller

so its value was not

null

but

transdecoder

. I believe in this case, the file names are wrong. Maybe there should be a checkpoint either

orf-caller

user-orfs-name

to be used. need a bug? thanks.

Daniel Lundin

05/14/2025, 8:39 AM

I thought I had fixed this...

orf_caller

doesn't have a default in the current version (but the docs say differently). Which version did you run?

Mehrdad Jaberi

05/14/2025, 8:39 AM

dev

Mehrdad Jaberi

05/14/2025, 8:40 AM

but on a rerun I unset the

orf-caller

and the output files are correctly named.

Daniel Lundin

05/14/2025, 8:40 AM

Right, then your output files should have

user_orfs

in their names, unless you set

--user_orfs_name

to something else.

Daniel Lundin

05/14/2025, 8:41 AM

(My reply was before I saw your latest comment.)

👍 1

Daniel Lundin

05/14/2025, 8:43 AM

As I've been into before, I'm fond of our output in the

summary_tables

directory, so this is what I automatically check. I might hence, again, miss naming in the other output directories.

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