feat2-0, no concatenation of fastqs

I am running the feat2-0 branch version of the pipeline. I give the same sample and group names to 2 fastq files in order to concatenate them. This doesn't happen and the 2 samples are treated separately. The pipeline fails at Process NFCORE_CLIPSEQ:CLIPSEQ:CONSENSUS_CROSSLINKS_CAT_CAT as there is collision between the sample names.

Steps to reproduce

Steps to reproduce the behaviour:

Command line: ../clipseq/main.nf -c KCL-CREATE_interruptible.config --input samplesheet.csv
--source "fastq" --fasta "Homo_sapiens.GRCh38.fasta" --gtf "Homo_sapiens.GRCh38.109.gtf" --ncrna_fasta "Homo_sapiens.GRCh38.smrna.fasta"

##Error

ERROR ~ Error executing process > 'NFCORE_CLIPSEQ:CLIPSEQ:CONSENSUS_CROSSLINKS_CAT_CAT'

Caused by:
Process NFCORE_CLIPSEQ:CLIPSEQ:CONSENSUS_CROSSLINKS_CAT_CAT input file name collision -- There are multiple input files for each of the following file names: input3.genome.xl.bed

##Samplesheet:
sample_name,group_name,input_name,fastq IP_R3_T1,IP,input,../ultraplex_demux_WT_C_20230124_Fwd.fastq.gz IP_R4_T1,IP,input,../ultraplex_demux_WT_D_20230124_Fwd.fastq.gz input2,input,,../ultraplex_demux_input_SP3_temp_WT_B_20230124_Fwd.fastq.gz input3,input,,../ultraplex_demux_input_SP3_temp_WT_C_20230124_Fwd.fastq.gz input3,input,,../ultraplex_demux_input_SP3_temp_WT_D_20230124_Fwd.fastq.gz

System

• Hardware: HPC
• Executor: slurm
• Engine: Singularity

Start with main.nf and the samplesheet handling used by the CONSENSUS_CROSSLINKS_CAT_CAT process, using the supplied command and configuration to reproduce the collision. Trace how repeated sample_name and group_name entries are represented before that process. Done means the two matching FASTQ inputs are concatenated and the pipeline no longer reports an input file name collision.