scipipe_proc_init_api.go

// -------------------------
// Option A
// -------------------------
merge := wf.NewProc("merge_"+ind, "bwa sampe {i:ref} {i:sai1} {i:sai2} {i:fq1} {i:fq2} > {o:merged} # {i:refdone} {p:ind}",
merge.InParam("ind").FromStr(ind)
merge.In("ref").From(ungzipRef.Out("out"))
merge.In("refdone").From(indexRef.Out("done"))
merge.In("sai1").From(outs[ind]["1"]["sai"])
merge.In("sai2").From(outs[ind]["2"]["sai"])
merge.In("fq1").From(outs[ind]["1"]["fastq"])
merge.In("fq2").From(outs[ind]["2"]["fastq"])
merge.SetOut("merged", "{p:ind}.merged.sam")
		    
// -------------------------
// Option B
// -------------------------
merge := wf.NewProc("merge_"+ind, "bwa sampe {i:ref} {i:sai1} {i:sai2} {i:fq1} {i:fq2} > {o:merged} # {i:refdone} {p:ind}",
	sp.ParamSpec{
		"ind": sp.ParamFromStr(ind),
	},
	sp.InSpec{
		"ref": ungzipRef.Out("out"),
		"refdone": indexRef.Out("done"),
		"sai1": outs[ind]["1"]["sai"],
		"sai2": outs[ind]["2"]["sai"],
		"fq1": outs[ind]["1"]["fastq"],
		"fq2": outs[ind]["1"]["fastq"],
	},
	sp.OutSpec{
		"merged": "{p:ind}.merged.sam",	
	})

// -------------------------
// Option C
// -------------------------
merge := wf.NewProc("merge_"+ind, "bwa sampe {i:ref} {i:sai1} {i:sai2} {i:fq1} {i:fq2} > {o:merged} # {i:refdone} {p:ind}")
merge.InFrom(sp.InSpec{
	"ref": ungzipRef.Out("out"),
	"refdone": indexRef.Out("done"),
	"sai1": outs[ind]["1"]["sai"],
	"sai2": outs[ind]["2"]["sai"],
	"fq1": outs[ind]["1"]["fastq"],
	"fq2": outs[ind]["1"]["fastq"],
})
merge.ParamsFrom(sp.ParamsSpec{
	"ind": sp.ParamFromStr(ind),
})
merge.SetOuts(sp.OutSpec{
	"merged": "{p:ind}.merged.sam",	
})