Changes to CITATIONS and testing for the tupled env

sanger-tol · Jul 17, 2024 · 8b72624 · 8b72624
1 parent c733f15
commit 8b72624
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Showing 3 changed files with 19 additions and 16 deletions.
diff --git a/CITATION.cff b/CITATION.cff
@@ -9,21 +9,24 @@ message: >-
 type: software
 authors:
     - given-names: Damon-Lee Bernard
-        family-names: Pointon
-        affiliation: Wellcome Sanger Institute
-        orcid: "https://orcid.org/0000-0003-2949-6719"
+      family-names: Pointon
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0003-2949-6719"
     - given-names: Matthieu
-        family-names: Muffato
-        affiliation: Wellcome Sanger Institute
-        orcid: "https://orcid.org/0000-0002-7860-3560"
+      family-names: Muffato
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0002-7860-3560"
     - given-names: Ying
-        family-names: Sims
-        affiliation: Wellcome Sanger Institute
-        orcid: "https://orcid.org/0000-0003-4765-4872"
+      family-names: Sims
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0003-4765-4872"
     - given-names: William
-        family-names: Eagles
-        affiliation: Wellcome Sanger Institute
-        orcid: "https://orcid.org/0009-0006-9956-0404"
+      family-names: Eagles
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0009-0006-9956-0404"
+identifiers:
+    - type: doi
+      value: 10.5281/zenodo.XXXXXXX
 repository-code: "https://github.com/sanger-tol/curationpretext"
 license: MIT
 commit: TODO

diff --git a/modules/local/get_largest_scaff.nf b/modules/local/get_largest_scaff.nf
@@ -12,8 +12,8 @@ process GET_LARGEST_SCAFF {
     tuple val(meta), path(file)
 
     output:
-    env largest_scaff   , emit: scaff_size
-    path "versions.yml" , emit: versions
+    tuple val(meta), env(largest_scaff),    emit: scaff_size
+    path "versions.yml",                    emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/subworkflows/local/accessory_files.nf b/subworkflows/local/accessory_files.nf
@@ -46,15 +46,15 @@ workflow ACCESSORY_FILES {
     //
     GAP_FINDER (
         reference_tuple,
-        GET_LARGEST_SCAFF.out.scaff_size.toInteger()
+        GET_LARGEST_SCAFF.out.scaff_size.map{it -> it[0].toInteger()}
     )
     ch_versions = ch_versions.mix(GAP_FINDER.out.versions)
 
     //
     // SUBWORKFLOW: GENERATE TELOMERE WINDOW FILES WITH LONGREAD READS AND REFERENCE
     //
     TELO_FINDER (
-        GET_LARGEST_SCAFF.out.scaff_size,
+        GET_LARGEST_SCAFF.out.scaff_size.map{it -> it[0].toInteger()},
         reference_tuple,
         params.teloseq
     )