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lines changed Original file line number Diff line number Diff line change @@ -331,16 +331,16 @@ _Before:_
331331
332332``` groovy title="hello-operators.nf" linenums="52"
333333 output:
334- path "${input_bam}.vcf"
335- path "${input_bam}.vcf.idx"
334+ path "${input_bam}.vcf" , emit: vcf
335+ path "${input_bam}.vcf.idx" , emit: idx
336336```
337337
338338_ After:_
339339
340340``` groovy title="hello-operators.nf" linenums="52"
341341 output:
342- path "${input_bam}.g.vcf"
343- path "${input_bam}.g.vcf.idx"
342+ path "${input_bam}.g.vcf" , emit: vcf
343+ path "${input_bam}.g.vcf.idx" , emit: idx
344344```
345345
346346### 1.3. Run the pipeline again
@@ -773,8 +773,8 @@ _After:_
773773
774774``` groovy title="hello-operators.nf" linenums="87"
775775output:
776- path "${cohort_name}.joint.vcf"
777- path "${cohort_name}.joint.vcf.idx"
776+ path "${cohort_name}.joint.vcf" , emit: vcf
777+ path "${cohort_name}.joint.vcf.idx" , emit: idx
778778```
779779
780780We're almost done!
Original file line number Diff line number Diff line change @@ -331,8 +331,8 @@ process GATK_JOINTGENOTYPING {
331331 path ref_dict
332332
333333 output:
334- path "${cohort_name}.joint.vcf"
335- path "${cohort_name}.joint.vcf.idx"
334+ path "${cohort_name}.joint.vcf" , emit: vcf
335+ path "${cohort_name}.joint.vcf.idx" , emit: idx
336336
337337 script:
338338 def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ')
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