fastq filename convention and sample name parsing

[janprovaz]

Hi Everyone!

Sample name is parsed by splitting the filename on _.
This breaks when the sample names are different from xxxx_L001_R{1,2}_001fastq.gz or has an unexpected lack of _
In the documentation it is not obvious, that one should have the _L001_ in the filename.

I had samples named G0-3-2_R1_001.fastq.gz with the G0-3-2 being different sample names (only the numbers varied, single digits in all cases).

Running with default parameters:
./nextflow run nf-core/ampliseq -profile singularity --input reads --FW_primer GTGCCAGCMGCCGCGGTAA --RV_primer GGACTACHVGGGTWTCTAAT --metadata metadata.txt

Resulted in:

Error executing process > 'multiqc (1)'
Caused by:
 Process `multiqc` input file name collision -- There are multiple input files for each of the following file names: cutadapt/logs/cutadapt_log_.txt

notice the absence of the sample name in the file cutadapt_log_.txt

I renamed the input samples to:
G032_L001_R1_001.fastq.gz and it went through.
G0-3-2_L001_R1_001.fastq.gz also tested and also worked.

Proposed change:
Altering the documentation to reflect this, or changing the way the filenames are parsed in main.nf

Hope this helps 😄
Thank you for your amazing work!
All the best,
Jan

[erikrikarddaniel]

This behaviour reflects how QIIME2 parses file names. For other file name patterns, you can use the --manifest option.

Documentation in ampliseq can probably be improved as you suggest.

[janprovaz]

Thank you, Daniel! Perfect :) 👍

[d4straub]

Actually, I think it should work with --input. The problem seems that the name (not read file, but the "pair_id" determined by e.g. .fromFilePairs) is splitted by _ here but no _ is found in the case you mention and therefore no name is given. I am not sure why I never came across that case!

edit: _L001_ or similar is not required. The pipeline produces internally manifests to import read files to QIIME2 to make naming more flexible. Any _ should do the job. The PR below allows now improves that behavior and will work on the filenames you mention.

[d4straub]

Fixed in dev.