Remove unnecessary .view() in subworkflows/nf-core/vcf_phase_shapeit5…

… & tests/modules/nf-core/shapeit5/ligate/main.nf (nf-core#5280) * .view() deleted * Delete unecessary view * Update licence * Bcftools view compressed output * Update licence --------- Co-authored-by: Dimple Adiwal <[email protected]> Co-authored-by: Dimple Adiwal <[email protected]> Co-authored-by: Louis LE NEZET <[email protected]>
famosab · Mar 20, 2024 · dcf17cc · dcf17cc
1 parent 61f2ea5
commit dcf17cc
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Showing 5 changed files with 6 additions and 7 deletions.
diff --git a/modules/nf-core/shapeit5/ligate/meta.yml b/modules/nf-core/shapeit5/ligate/meta.yml
@@ -12,8 +12,8 @@ tools:
       homepage: "https://odelaneau.github.io/shapeit5/"
       documentation: "https://odelaneau.github.io/shapeit5/docs/documentation"
       tool_dev_url: "https://github.com/odelaneau/shapeit5"
-      doi: "10.1101/2022.10.19.512867 "
-      licence: "['MIT']"
+      doi: "10.1101/2022.10.19.512867"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

diff --git a/subworkflows/nf-core/vcf_phase_shapeit5/main.nf b/subworkflows/nf-core/vcf_phase_shapeit5/main.nf
@@ -66,10 +66,9 @@ workflow VCF_PHASE_SHAPEIT5 {
 
     ch_ligate_input = SHAPEIT5_PHASECOMMON.out.phased_variant
         .join(VCF_INDEX1.out.csi, failOnMismatch:true, failOnDuplicate:true)
-        .view()
         .map{ meta, vcf, csi ->
             newmeta = meta + [id: meta.id.split("_")[0..-2].join("_")]
-            [newmeta, vcf, csi]}.view()
+            [newmeta, vcf, csi]}
         .combine(ch_chunks_number, by:0)
         .map{meta, vcf, csi, chunks_num ->
             [groupKey(meta, chunks_num), vcf, csi]}

diff --git a/tests/modules/nf-core/shapeit5/ligate/main.nf b/tests/modules/nf-core/shapeit5/ligate/main.nf
@@ -32,7 +32,7 @@ workflow test_shapeit5_ligate {
     phase_input = Channel.of([[ id:'NA12878_1X']])
                         .combine(BCFTOOLS_VIEW.out.vcf.collect().map{it[1]})
                         .combine(BCFTOOLS_INDEX.out.csi.collect().map{it[1]})
-                        .combine(sample).view()
+                        .combine(sample)
                         .combine(region)
                         .map{ meta, vcf, csi, sample, region ->
                             [meta + [region: region.replace(":","_")],
@@ -43,7 +43,6 @@ workflow test_shapeit5_ligate {
 
     phased_variant = SHAPEIT5_PHASECOMMON.output.phased_variant
                         .map{ meta, vcf -> [meta.subMap(["id"]), vcf]}
-                        .view()
 
     BCFTOOLS_INDEX2 ( phased_variant )
 
@@ -55,6 +54,5 @@ workflow test_shapeit5_ligate {
                                 a.getName() <=> b.getName()},
                             csi]}
 
-    ligate_input.view()
     SHAPEIT5_LIGATE ( ligate_input )
 }
diff --git a/tests/modules/nf-core/shapeit5/ligate/nextflow.config b/tests/modules/nf-core/shapeit5/ligate/nextflow.config
@@ -1,6 +1,7 @@
 process {
     withName: BCFTOOLS_VIEW {
         ext.args = [
+            "-Oz",
             "-e 'GT=\"./.\"||GT=\".\"'"
         ].join(' ')
         ext.prefix = { "${meta.id}" }

diff --git a/tests/subworkflows/nf-core/vcf_phase_shapeit5/nextflow.config b/tests/subworkflows/nf-core/vcf_phase_shapeit5/nextflow.config
@@ -5,6 +5,7 @@ process {
     }
     withName: BCFTOOLS_VIEW {
         ext.args = [
+            "-Oz",
             "-e 'GT=\"./.\"||GT=\".\"'"
         ].join(' ')
     }