Remove filter in samtools coverage

Author: merszym

assets/pipeline/meta.tsv

@@ -1,2 +1,2 @@
 id	RG	ReadsRaw	ReadsFiltered	ReadsLengthfiltered	SpeciesKmers	KmerCoverage	KmerDupRate	ExtractLVL	ReadsExtracted	Order	Family	Species	Reference	ReadsMapped	ProportionMapped	ReadsDeduped	DuplicationRate	CoveredBP	ReadsBedfiltered	PostBedCoveredBP	FamPercentage	Ancientness	ReadsDeam(1term)	ReadsDeam(3term)	Deam5(95ci)	Deam3(95ci)	Deam5Cond(95ci)	Deam3Cond(95ci)	MeanFragmentLength	MeanFragmentLength(3term)	Coverage	Breadth	ExpectedBreadth	ProportionExpectedBreadth
--	-	0	0	0	0	0	0	-	0	-	-	-	best	0	0	0	0	0	-	-	-	-	-	-	-	-	-	-	0	0	0	0	0	0
+-	-	0	0	0	0	0	0	-	0	-	-	-	best	0	0	0	0	0	-	-	-	-	-	-	-	-	-	-	0	0	0	0.0	0.0	

main.nf

@@ -317,7 +317,6 @@ workflow {
         .groupTuple(by:[0,1])   //[[rg, fam, [covered_bp < .. < covered_bp][meta,meta,meta],[bam,bam,bam]]
         .map{n -> [n[3][-1], n[4][-1]]} // from the highest, the [meta, bam]
 
-    best.view()
     //
     // 7. Run Intersect Bed
     //

modules/local/samtools_coverage/main.nf

@@ -13,7 +13,7 @@ process SAMTOOLS_COVERAGE {
 
     script:
     """
-    samtools coverage -H ${bam} | cut -f 5-7
+    samtools coverage -H ${bam} --ff UNMAP | cut -f 5-7
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":