Hi there I m trying to implement grouping of samples but I m nf-core #multiqc

Hi there, I'm trying to implement grouping of samp...

Lucille Augusta

12/16/2024, 11:08 AM

Hi there, I'm trying to implement grouping of samples, but I'm not able to expand the row in the general stats. Likely, because I have the columns duplicated, but also not sure how to solve this. My config file:

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extra_fn_clean_exts:
    - '_R1'
    - '_R2'
    - '.sorted'

fn_clean_exts:
  - ".txt"
  - ".bz"
  - ".gz"
  - ".fastq"
  - ".fastq.gz"

table_sample_merge:
  "Read 1, raw": "_raw_1"
  "Read 1, trim": "_trim_1"
  "Read 2, raw": "_raw_2"
  "Read 2, trim": "_trim_2"
  "Single-end, raw": "_raw"
  "Single-end, trim": "_trim"

I hope you have some input 🙂 Thanks, Lucille

Phil Ewels

12/16/2024, 11:19 AM

What is it that you're expecting here? The two different datasets showing as a single row?

Phil Ewels

12/16/2024, 11:20 AM

If so then

table_sample_merge

needs to resolve them into a single shared sample name, so handle the

and

suffixes

Phil Ewels

12/16/2024, 11:21 AM

Otherwise I wonder if you mean that the rows are showing properly but the underlying data isn't visible? In which case it's likely because you're merging the samples already in

extra_fn_clean_exts

and so by the time it gets to

table_sample_merge

you only have one value

Phil Ewels

12/16/2024, 11:21 AM

Side note:

extra_fn_clean_exts

and

fn_clean_exts

do the same thing. It's just that the latter clobbers the defaults and the former appends to them.

Phil Ewels

12/16/2024, 11:22 AM

If it's the second thing then try just removing the

extra_fn_clean_exts

and

fn_clean_exts

config sections

Lucille Augusta

12/16/2024, 12:20 PM

Thanks for the reply. After removing

extra_fn_clean_exts

and

fn_clean_exts

the report looks the same. For each dataset I have forward and reverse reads + trimmed version, I was expecting these to show as expanded rows per. dataset and not in multiple columns (eg. 4 x "CG")

Phil Ewels

12/16/2024, 12:38 PM

oh I see, I didn't notice the multiple columns before sorry

Phil Ewels

12/16/2024, 12:38 PM

weird, are you able to share a minimal reproducible example that I can run myself please?

Lucille Augusta

12/16/2024, 2:27 PM

multiqc_test.tar.gz

Lucille Augusta

12/16/2024, 2:28 PM

Maybe you're able to see it from here? 🙂

Phil Ewels

12/18/2024, 10:49 PM

Apologies, ran out of time to look at this on Monday and not much better now. Could you put this into a post on community.seqera.io/multiqc so that others can have a look?

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