Description of the bug

Hello, thanks for a great pipeline. I noticed in my recent run (v3.19.0-g0bb032c) that my bigwig files (from reverse stranded libraries) seem to be mislabeled after viewing a couple genes on IGV. My previous run with similar samples (v3.14.0 when the bedgraph generation was in only 1 process - not split into FW/REV) did not have this issue.

I believe this may be due to how the file prefixes are assigned in the config.

Example commands from my execution report:

# NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (Patient_Ref_1)
bedtools \
    genomecov \
    -ibam Patient_Ref_1.markdup.sorted.bam \
    -split -du -strand + -bg \
    | LC_ALL=C sort --parallel=1 --buffer-size=3G -k1,1 -k2,2n \
    > Patient_Ref_1.reverse.bedGraph

# NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (Patient_Ref_1)
bedClip \
    Patient_Ref_1.reverse.bedGraph \
    Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.sizes \
    Patient_Ref_1.clip.forward.bedGraph

Command used and terminal output

Relevant files

No response

System information

No response