From 8b72624ca6962bbe794f813365a1541948af977e Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Wed, 17 Jul 2024 12:01:02 +0100
Subject: [PATCH] Changes to CITATIONS and testing for the tupled env

---
 CITATION.cff                          | 27 +++++++++++++++------------
 modules/local/get_largest_scaff.nf    |  4 ++--
 subworkflows/local/accessory_files.nf |  4 ++--
 3 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index ead007f..8a0ff1c 100644
--- 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
index 6746e21..604db03 100755
--- 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
index f0378bc..a371235 100755
--- a/subworkflows/local/accessory_files.nf
+++ b/subworkflows/local/accessory_files.nf
@@ -46,7 +46,7 @@ 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)
 
@@ -54,7 +54,7 @@ workflow ACCESSORY_FILES {
     // 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
     )