Sample merging does not work if files are named the same

[nick-youngblut]

Description of the bug

The docs state:

Multiple runs of the same sample
The sample identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes:

The merging does not work if the fastq file paths have the same file name (basename). For example:

sample,fastq_1,fastq_2
sample1,run1/sample1_R1.fastq.gz,run1/sample1_R2.fastq.gz
sample1,run2/sample1_R1.fastq.gz,run2/sample1_R2.fastq.gz

This naming scheme will generate the following error:

Process `NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC` input file name collision -- There are multiple input files for each of the following file names: sample1_R1.fastq.gz, sample1_R1.fastq.gz

It appears that NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC is run on all fastq files separately instead of only after merging by sample, and the process stages just by the sample sheet file names (e.g., sample1_R1.fastq.gz instead of run1/sample1_R1.fastq.gz), which results in the naming collision.

Given that many users will likely have the same fastq file naming for multiple sequencing runs (as in my example), it would be very helpful if users did not have to make sure that the fastq file names are unique across runs.

Command used and terminal output

No response

Relevant files

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System information

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