samplesheet handling: different path + same filename gives an error

[AdrijaK]

Description of the bug

Hi all, I have encountered a buggy behaviour in samplesheet processing:

My samplesheet has specified absolute paths to different files (/path/to/run_01/ and /path/to/run_02/) with same filename: this is typical for pooling re-sequencing libraries:

cat samplesheet-nfcore.csv

sample,fastq_1,fastq_2
Sample1_rep1,/path/to/run_01/Sample1_R1.fastq.gz,/path/to/run_01/Sample1_R2.fastq.gz
Sample1_rep1,/path/to/run_02/Sample1_R1.fastq.gz,/path/to/run_02/Sample1_R2.fastq.gz
Sample2_rep1,/path/to/run_01/Sample2_R1.fastq.gz,/path/to/run_01/Sample2_R2.fastq.gz
Sample2_rep1,/path/to/run_02/Sample2_R1.fastq.gz,/path/to/run_02/Sample2_R2.fastq.gz

Command used and terminal output

nextflow run nf-core/methylseq -profile ku_sund_danhead,dancmpn01fl -r 2.6.0 -params-file nfcore-methylseq-params.yaml --outdir GRCm38 --genome GRCm38 --aligner bismark

ERROR ~ Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQC (16)'

Caused by:
  Process `NFCORE_METHYLSEQ:METHYLSEQ:FASTQC` input file name collision -- There are multiple input files for each of the following file names: Sample1_R1.fastq.gz, Sample1_R2.fastq.gz

Relevant files

No response

System information

Nextflow version 23.10.1 Hardware: HPC Executor: slurm Container engine: Singularity OS: Red Hat Enterprise Linux 8.9 (Ootpa) Version of nf-core/methylseq v2.6.0-g54f823e