Pipeline prefixes X to samplenames

[RaverJay]

Description of the bug

Running the pipeline with this samplesheet.csv:

sample,fastq_1,fastq_2,strandedness,condition,replicate
1A2,reads/1A2_S4_R1_001.fastq.gz,reads/1A2_S4_R2_001.fastq.gz,auto,1,A2
1B2,reads/1B2_S14_R1_001.fastq.gz,reads/1B2_S14_R2_001.fastq.gz,auto,1,B2
1C1,reads/1C1_S24_R1_001.fastq.gz,reads/1C1_S24_R2_001.fastq.gz,auto,1,C1
5A2,reads/5A2_S7_R1_001.fastq.gz,reads/5A2_S7_R2_001.fastq.gz,auto,5,A2
5B2,reads/5B2_S17_R1_001.fastq.gz,reads/5B2_S17_R2_001.fastq.gz,auto,5,B2
5C1,reads/5C1_S27_R1_001.fastq.gz,reads/5C1_S27_R2_001.fastq.gz,auto,5,C1

yielded these tables:

salmon.merged.gene_counts.tsv

gene_id gene_name   X1A2    X1B2    X1C1    X5A2    X5B2    X5C1
16Sa    16Sa    11039.388   14.242  0   0   0   0
16Sb    16Sb    19419.287   13587.814   9855.454    330.904 4258.272    924.453
...

Why were samples renamed?

Cheers

Command used and terminal output

No response

Relevant files

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System information

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