Skipping NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_ALIGN

[aboddicker]

Skipping NFCORE_MAG:MAG:BOWTIE2_PHIX_REMOVAL_ALIGN

[d4straub]

Why not use --keep_phix ? This should not run the process you are disliking, see

mag/workflows/mag.nf

Lines 275 to 287 in a50117e

	if(!params.keep_phix) {
	BOWTIE2_PHIX_REMOVAL_BUILD (
	ch_phix_db_file
	)
	BOWTIE2_PHIX_REMOVAL_ALIGN (
	ch_short_reads_hostremoved,
	BOWTIE2_PHIX_REMOVAL_BUILD.out.index
	)
	ch_short_reads_phixremoved = BOWTIE2_PHIX_REMOVAL_ALIGN.out.reads
	ch_versions = ch_versions.mix(BOWTIE2_PHIX_REMOVAL_ALIGN.out.versions.first())
	} else {
	ch_short_reads_phixremoved = ch_short_reads_hostremoved
	}

[aboddicker]

Closing ticket. --keep_phix skips initial Bowtie2 alignment of reads to PhiX reference.

[jfy133]

Related: #455

[jfy133]

Yeah I forgot about that (I guess possibly the reason why @aboddicker also didn't recognise it, I find it rather unintuitive 😅 ) - please let us know if that works @aboddicker ! Then we close that and refer to the other issue for making the method of opting in/out more consistent

[aboddicker]

Thanks so much! Yes, this is a great solution. Selecting --keep_phix bypasses the alignment and proceeds simultaneously with FastQC and into assembly upon launch.