MERGE_CFF not performed for certain samples

[anoronh4]

Description of the bug

currently MERGE_CFF is not kicking off for certain samples even though upstream processes STARFUSION_TO_CFF, ARRIBA_TO_CFF and FUSIONCATCHER_TO_CFF have completed for a given sample. The issue seems to be occurring here:

forte/subworkflows/local/fusion.nf

Lines 101 to 111 in d38564e

	MERGE_CFF(
	ARRIBA_TO_CFF.out.cff
	.map{ meta, file -> [meta, file]}
	.mix(
	FUSIONCATCHER_TO_CFF.out.cff
	.map{ meta, file -> [meta, file]}
	).mix(
	STARFUSION_TO_CFF.out.cff
	.map{ meta, file -> [meta, file]}
	).groupTuple(by:[0],size:numcallers),
	)

with the mix operators working correctly but the groupTuple operation is not emitting the expected result each time. confusingly, resumed runs will have different samples running MERGE_CFF and other samples that never launch the task.

after some troubleshooting i found that the error originates from inconsistent values in the meta map, specifically read_group and fastq_pair_id. since the meta map is used as the key in the groupTuple operation, it needs to be consistent across each sample. The value is inconsistent because it is how it is grouped in another subworkflow:

forte/subworkflows/local/group_reads.nf

Lines 8 to 19 in 0b3d927

	grouped_reads = ungrouped_reads
	.map{ meta, reads ->
	def read_group = meta.read_group
	def fastq_pair_id = meta.fastq_pair_id
	def meta_clone = meta.clone().findAll { !["read_group","fastq_pair_id"].contains(it.key) }
	meta_clone.id = meta.sample
	[groupKey(meta_clone,meta.fq_num), reads, read_group, fastq_pair_id]
	}.groupTuple(by:[0])
	.map{ meta, reads, read_group, fastq_pair_id ->
	meta = meta + [read_group:read_group.join(','), fastq_pair_id:fastq_pair_id.join(',')]
	[meta, reads.flatten()]
	}

here read_group and fastq_pair_id in the meta map is replaced after grouping with a string that concatenates the read group and fastq pair ids strings. they are sometimes not concatenated in the same order. sort() is expected to fix the problem.

Command used and terminal output

Relevant files

No response

System information

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