Flipped bigwig strands in PROseq samples

[Caffeinated-Code]

Description of the bug

Hi Edmund,
I am raising a ticket here for the strand-flipping issue I mentioned on slack.

Bug:
BigWigs generated for PROseq samples appear to be flipped. The strand carrying the gene body signal is inconsistent with gene direction.
Example: GUSB gene on the negative strand. Genebody signal in the public Jurkat sample processed with the v2.1.1 pipeline is on the positive strand (UCSC Browser view attached).
The same issue was observed in internal PROseq samples as well.

Command used and terminal output

nextflow run nf-core/nascent -profile docker --input /home/ec2-user/environment/sampleSheets/sampleSheet.public_Jurkat.202306.csv \
    --assay_type PROseq \
    --tracedir ./pipeline_info \
    --fasta /home/ec2-user/environment/annotations/bwa/hg38as.fa \
    --bwa_index /home/ec2-user/environment/annotations/bwa \
    --gtf /home/ec2-user/environment/annotations/gencode.v38.chr_patch_hapl_scaff.annotation.gtf 
    --filter_bed /home/ec2-user/environment/annotations/hg38as.blacklist.ENCODEDCC.bed \
    -w /data/work --outdir /data/outdir/public.Jurkat.GSE66031/ -resume > public.Jurkat.202306.log 2>&1

Relevant files

System information

Nextflow version: 23.04.1
Hardware : AWS Cloud9
Executor : Local
Container engine : Docker
OS:
Nascent pipeline version: v2.1.1-g9ff33c7

[edmundmiller]

Sweet thanks, I was just about to make an issue for this!

These are the config pieces that control that

nascent/conf/modules.config

Lines 110 to 118 in 9cba10b

	withName: BEDTOOLS_GENOMECOV_PLUS {
	ext.args = "-bg -strand +"
	ext.prefix = { "${meta.id}.plus" }
	}
	withName: BEDTOOLS_GENOMECOV_MINUS {
	ext.args = "-bg -strand -"
	ext.prefix = { "${meta.id}.minus" }
	}

These look like the two relevant sections of the script linked, and it doesn't look like I got the -strand flipped or the naming...
https://github.com/Danko-Lab/proseq2.0/blob/e306ae4722639cf44b0074cbdf1285e53a0ae9e7/proseq2.0.bsh#L868-L882
https://github.com/Danko-Lab/proseq2.0/blob/e306ae4722639cf44b0074cbdf1285e53a0ae9e7/proseq2.0.bsh#L1143-L1156

[edmundmiller]

Relevant sections for flipping proseq(@Caffeinated-Code):
https://github.com/Danko-Lab/proseq2.0/blob/e306ae4722639cf44b0074cbdf1285e53a0ae9e7/proseq2.0.bsh#L829-L857
https://github.com/Danko-Lab/proseq2.0/blob/e306ae4722639cf44b0074cbdf1285e53a0ae9e7/proseq2.0.bsh#L863-L866