From edec19bb9562065996a1b9ca11f5073c5a4fa597 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 20 Nov 2024 20:08:49 +0000
Subject: [PATCH] Replace numeric with named outputs for GATK_HAPLOTYPECALLER
 (#471)

---
 hello-nextflow/hello-config/main.nf                         | 4 ++--
 hello-nextflow/hello-modules/main.nf                        | 4 ++--
 hello-nextflow/hello-nf-test/main.nf                        | 6 +++---
 hello-nextflow/solutions/hello-config/final-main.nf         | 4 ++--
 hello-nextflow/solutions/hello-modules/final-main.nf        | 4 ++--
 .../solutions/hello-operators/hello-operators-2.nf          | 4 ++--
 .../solutions/hello-operators/hello-operators-3.nf          | 4 ++--
 7 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/hello-nextflow/hello-config/main.nf b/hello-nextflow/hello-config/main.nf
index 49e2c4ef..755b5545 100644
--- a/hello-nextflow/hello-config/main.nf
+++ b/hello-nextflow/hello-config/main.nf
@@ -133,8 +133,8 @@ workflow {
     )
 
     // Collect variant calling outputs across samples
-    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out[0].collect()
-    all_idxs_ch = GATK_HAPLOTYPECALLER.out[1].collect()
+    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect()
+    all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect()
 
     // Combine GVCFs into a GenomicsDB data store and apply joint genotyping
     GATK_JOINTGENOTYPING(
diff --git a/hello-nextflow/hello-modules/main.nf b/hello-nextflow/hello-modules/main.nf
index 9904e2cf..316b0c3a 100644
--- a/hello-nextflow/hello-modules/main.nf
+++ b/hello-nextflow/hello-modules/main.nf
@@ -117,8 +117,8 @@ workflow {
     )
 
     // Collect variant calling outputs across samples
-    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out[0].collect()
-    all_idxs_ch = GATK_HAPLOTYPECALLER.out[1].collect()
+    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect()
+    all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect()
 
     // Combine GVCFs into a GenomicsDB data store and apply joint genotyping
     GATK_JOINTGENOTYPING(
diff --git a/hello-nextflow/hello-nf-test/main.nf b/hello-nextflow/hello-nf-test/main.nf
index a4f58868..8d380487 100644
--- a/hello-nextflow/hello-nf-test/main.nf
+++ b/hello-nextflow/hello-nf-test/main.nf
@@ -27,10 +27,10 @@ workflow {
         ref_dict_file,
         intervals_file
     )
-
+    
     // Collect variant calling outputs across samples
-    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out[0].collect()
-    all_idxs_ch = GATK_HAPLOTYPECALLER.out[1].collect()
+    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect()
+    all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect()
 
     // Combine GVCFs into a GenomicsDB data store and apply joint genotyping
     GATK_JOINTGENOTYPING(
diff --git a/hello-nextflow/solutions/hello-config/final-main.nf b/hello-nextflow/solutions/hello-config/final-main.nf
index 8aa9e3d8..0f46c1da 100644
--- a/hello-nextflow/solutions/hello-config/final-main.nf
+++ b/hello-nextflow/solutions/hello-config/final-main.nf
@@ -117,8 +117,8 @@ workflow {
     )
 
     // Collect variant calling outputs across samples
-    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out[0].collect()
-    all_idxs_ch = GATK_HAPLOTYPECALLER.out[1].collect()
+    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect()
+    all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect()
 
     // Combine GVCFs into a GenomicsDB data store and apply joint genotyping
     GATK_JOINTGENOTYPING(
diff --git a/hello-nextflow/solutions/hello-modules/final-main.nf b/hello-nextflow/solutions/hello-modules/final-main.nf
index a4f58868..3e55a0d1 100644
--- a/hello-nextflow/solutions/hello-modules/final-main.nf
+++ b/hello-nextflow/solutions/hello-modules/final-main.nf
@@ -29,8 +29,8 @@ workflow {
     )
 
     // Collect variant calling outputs across samples
-    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out[0].collect()
-    all_idxs_ch = GATK_HAPLOTYPECALLER.out[1].collect()
+    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect()
+    all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect()
 
     // Combine GVCFs into a GenomicsDB data store and apply joint genotyping
     GATK_JOINTGENOTYPING(
diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-2.nf b/hello-nextflow/solutions/hello-operators/hello-operators-2.nf
index 130b5b20..a1dc8dfe 100644
--- a/hello-nextflow/solutions/hello-operators/hello-operators-2.nf
+++ b/hello-nextflow/solutions/hello-operators/hello-operators-2.nf
@@ -120,8 +120,8 @@ workflow {
     )
 
     // Collect variant calling outputs across samples
-    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out[0].collect()
-    all_idxs_ch = GATK_HAPLOTYPECALLER.out[1].collect()
+    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect()
+    all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect()
 
     // Combine GVCFs into a GenomicsDB datastore
     GATK_GENOMICSDB(
diff --git a/hello-nextflow/solutions/hello-operators/hello-operators-3.nf b/hello-nextflow/solutions/hello-operators/hello-operators-3.nf
index 4baf93f7..e3aaf6a8 100644
--- a/hello-nextflow/solutions/hello-operators/hello-operators-3.nf
+++ b/hello-nextflow/solutions/hello-operators/hello-operators-3.nf
@@ -130,8 +130,8 @@ workflow {
     )
 
     // Collect variant calling outputs across samples
-    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out[0].collect()
-    all_idxs_ch = GATK_HAPLOTYPECALLER.out[1].collect()
+    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect()
+    all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect()
 
     // Combine GVCFs into a GenomicsDB data store and apply joint genotyping
     GATK_JOINTGENOTYPING(