From b333f11af216b0c77f4f93af059180233418c268 Mon Sep 17 00:00:00 2001
From: Stephen Watts <hello@stephen.ac>
Date: Thu, 15 Aug 2024 12:49:10 +1000
Subject: [PATCH 1/3] Use consistent casing

---
 modules/local/chord/main.nf      | 4 ++--
 modules/local/linxreport/main.nf | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/chord/main.nf b/modules/local/chord/main.nf
index bd835166..91816c2e 100644
--- a/modules/local/chord/main.nf
+++ b/modules/local/chord/main.nf
@@ -70,8 +70,8 @@ process CHORD {
 
     sink('versions.yml')
     writeLines('"${task.process}":')
-    writeLines(paste('    CHORD:', packageVersion('CHORD')))
-    writeLines(paste('    mutSigExtractor:', packageVersion('mutSigExtractor')))
+    writeLines(paste('    chord:', packageVersion('CHORD')))
+    writeLines(paste('    mutsigextractor:', packageVersion('mutSigExtractor')))
     sink()
     """
 
diff --git a/modules/local/linxreport/main.nf b/modules/local/linxreport/main.nf
index f3d3a55e..0757ac75 100644
--- a/modules/local/linxreport/main.nf
+++ b/modules/local/linxreport/main.nf
@@ -37,7 +37,7 @@ process LINXREPORT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        R: \$(R --version | head -n1 | sed 's/^R version \\([0-9.]\\+\\).\\+/\\1/')
+        r: \$(R --version | head -n1 | sed 's/^R version \\([0-9.]\\+\\).\\+/\\1/')
         linxreport: \$(linxreport.R --version)
     END_VERSIONS
     """

From 5c3ca3af025fc5e199913676e5dc73976ff148d7 Mon Sep 17 00:00:00 2001
From: Stephen Watts <hello@stephen.ac>
Date: Thu, 15 Aug 2024 12:49:58 +1000
Subject: [PATCH 2/3] Add missed outputs into versions channel

---
 subworkflows/local/read_processing/main.nf | 2 ++
 workflows/targeted.nf                      | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/subworkflows/local/read_processing/main.nf b/subworkflows/local/read_processing/main.nf
index 4a0967ca..673d202e 100644
--- a/subworkflows/local/read_processing/main.nf
+++ b/subworkflows/local/read_processing/main.nf
@@ -92,6 +92,8 @@ workflow READ_PROCESSING {
         has_umis,
     )
 
+    ch_versions = ch_versions.mix(MARKDUPS.out.versions)
+
     // Sort into a tumor and normal channel
     ch_markdups_out = MARKDUPS.out.bam
         .branch { meta_markdups, bam, bai ->
diff --git a/workflows/targeted.nf b/workflows/targeted.nf
index f0b5649d..f2d4f0ba 100644
--- a/workflows/targeted.nf
+++ b/workflows/targeted.nf
@@ -99,6 +99,8 @@ workflow TARGETED {
     hmf_data = PREPARE_REFERENCE.out.hmf_data
     panel_data = PREPARE_REFERENCE.out.panel_data
 
+    ch_versions = ch_versions.mix(PREPARE_REFERENCE.out.versions)
+
     // Set GRIDSS config
     gridss_config = params.gridss_config !== null ? file(params.gridss_config) : hmf_data.gridss_config
 

From 8a87acebc84381285a0b584e7a669a0c494556fb Mon Sep 17 00:00:00 2001
From: Stephen Watts <hello@stephen.ac>
Date: Thu, 15 Aug 2024 12:50:13 +1000
Subject: [PATCH 3/3] Use consistent version mix invoke format

---
 workflows/wgts.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/workflows/wgts.nf b/workflows/wgts.nf
index 9facc5ac..0541966d 100644
--- a/workflows/wgts.nf
+++ b/workflows/wgts.nf
@@ -104,9 +104,7 @@ workflow WGTS {
     ref_data = PREPARE_REFERENCE.out
     hmf_data = PREPARE_REFERENCE.out.hmf_data
 
-    ch_versions = ch_versions.mix(
-        PREPARE_REFERENCE.out.versions,
-    )
+    ch_versions = ch_versions.mix(PREPARE_REFERENCE.out.versions)
 
     // Set GRIDSS config
     gridss_config = params.gridss_config !== null ? file(params.gridss_config) : hmf_data.gridss_config