From 6e4c2a5058f8d0b795a1de58abe5434146c61268 Mon Sep 17 00:00:00 2001
From: Riley-Grindle <122935497+Riley-Grindle@users.noreply.github.com>
Date: Wed, 11 Sep 2024 10:29:21 -0400
Subject: [PATCH] tidying modules perl script to report versions

---
 modules/local/doubletfinder.nf    | 2 +-
 modules/local/find_NN_clusters.nf | 2 +-
 modules/local/integration.nf      | 2 +-
 modules/local/makeseurat.nf       | 2 +-
 modules/local/merge.nf            | 2 +-
 modules/local/normalize_qc.nf     | 2 +-
 modules/local/plotting.nf         | 2 +-
 modules/local/runpca.nf           | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/modules/local/doubletfinder.nf b/modules/local/doubletfinder.nf
index b7ffe3f..c5813a6 100644
--- a/modules/local/doubletfinder.nf
+++ b/modules/local/doubletfinder.nf
@@ -41,7 +41,7 @@ process FIND_DOUBLETS {
         ${args}
 
     grep -i -E "R version " 02_${meta.id}_InitialVersions.log | perl -pe 's/ version /: "/g;s/ \(.*/"/g' >> 02_${meta.id}_FinalVersions.log
-    perl -ne 'print if /other attached packages:/ .. /^\$/' 02_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 02_${meta.id}_FinalVersions.log
+    perl -ne 'print if /other attached packages:/ .. /^\$/' 02_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 02_${meta.id}_FinalVersions.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/find_NN_clusters.nf b/modules/local/find_NN_clusters.nf
index 6e1e950..861991b 100644
--- a/modules/local/find_NN_clusters.nf
+++ b/modules/local/find_NN_clusters.nf
@@ -47,7 +47,7 @@ process FIND_NN_CLUSTER {
         ${args}
 
     grep -i -E "R version " 07_${meta}_InitialVersions.log | perl -pe 's/ version /: "/g;s/ \(.*/"/g' >> 07_${meta}_FinalVersions.log
-    perl -ne 'print if /other attached packages:/ .. /^\$/' 07_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 07_${meta}_FinalVersions.log
+    perl -ne 'print if /other attached packages:/ .. /^\$/' 07_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 07_${meta}_FinalVersions.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/integration.nf b/modules/local/integration.nf
index 29aca4c..551ddee 100644
--- a/modules/local/integration.nf
+++ b/modules/local/integration.nf
@@ -33,7 +33,7 @@ process INTEGRATION {
         ${args}
 
     grep -i -E "R version " 06_${meta}_InitialVersions.log | perl -pe 's/ version /: "/g;s/ \(.*/"/g' >> 06_${meta}_FinalVersions.log
-    perl -ne 'print if /other attached packages:/ .. /^\$/' 06_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 06_${meta}_FinalVersions.log
+    perl -ne 'print if /other attached packages:/ .. /^\$/' 06_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 06_${meta}_FinalVersions.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/makeseurat.nf b/modules/local/makeseurat.nf
index b4a857e..18b80ba 100644
--- a/modules/local/makeseurat.nf
+++ b/modules/local/makeseurat.nf
@@ -43,7 +43,7 @@ process MAKE_SEURAT {
     perl -i -pe 's/"//g;s/\\[\\d\\d?\\d?\\] //g' fileName.log *_Validation.log
 
     grep -i -E "R version " 00_${meta.id}_InitialVersions.log | perl -pe 's/ version /: "/g;s/ \(.*/"/g' >> 00_${meta.id}_FinalVersions.log
-    perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 00_${meta.id}_FinalVersions.log
+    perl -ne 'print if /other attached packages:/ .. /^\$/' 00_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 00_${meta.id}_FinalVersions.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/merge.nf b/modules/local/merge.nf
index 0794a3a..d401a4b 100644
--- a/modules/local/merge.nf
+++ b/modules/local/merge.nf
@@ -35,7 +35,7 @@ process MERGE_SO {
         ${args}
 
     grep -i -E "R version " 04_${meta}_InitialVersions.log | perl -pe 's/ version /: "/g;s/ \(.*/"/g' >> 04_${meta}_FinalVersions.log
-    perl -ne 'print if /other attached packages:/ .. /^\$/' 04_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 04_${meta.id}_FinalVersions.log
+    perl -ne 'print if /other attached packages:/ .. /^\$/' 04_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 04_${meta.id}_FinalVersions.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/normalize_qc.nf b/modules/local/normalize_qc.nf
index e72d6dc..d900ff8 100644
--- a/modules/local/normalize_qc.nf
+++ b/modules/local/normalize_qc.nf
@@ -56,7 +56,7 @@ process NORMALIZE_QC {
         ${args}
 
     grep -i -E "R version " 01_${meta.id}_InitialVersions.log | perl -pe 's/ version /: "/g;s/ \(.*/"/g' >> 01_${meta.id}_FinalVersions.log
-    perl -ne 'print if /other attached packages:/ .. /^\$/' 01_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 01_${meta.id}_FinalVersions.log
+    perl -ne 'print if /other attached packages:/ .. /^\$/' 01_${meta.id}_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 01_${meta.id}_FinalVersions.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/plotting.nf b/modules/local/plotting.nf
index 04be064..677bb87 100644
--- a/modules/local/plotting.nf
+++ b/modules/local/plotting.nf
@@ -51,7 +51,7 @@ process DISPLAY_REDUCTION {
         ${args}
 
     grep -i -E "R version " 08_${meta}_InitialVersions.log | perl -pe 's/ version /: "/g;s/ \(.*/"/g' >> 08_${meta}_FinalVersions.log
-    perl -ne 'print if /other attached packages:/ .. /^\$/' 08_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 08_${meta}_FinalVersions.log
+    perl -ne 'print if /other attached packages:/ .. /^\$/' 08_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 08_${meta}_FinalVersions.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/runpca.nf b/modules/local/runpca.nf
index 0d0e3f0..8b75045 100644
--- a/modules/local/runpca.nf
+++ b/modules/local/runpca.nf
@@ -32,7 +32,7 @@ process RUN_PCA {
         ${args}
 
     grep -i -E "R version " 05_${meta}_InitialVersions.log | perl -pe 's/ version /: "/g;s/ \(.*/"/g' >> 05_${meta}_FinalVersions.log
-    perl -ne 'print if /other attached packages:/ .. /^\$/' 05_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 05_${meta.id}_FinalVersions.log
+    perl -ne 'print if /other attached packages:/ .. /^\$/' 05_${meta}_InitialVersions.log | grep -v "other" | perl -pe 's/\\[.*]\s+//g;s/\s+/\n/g' | grep -v "^\$" | perl -pe 's/_/: "/g;s/\$/"/' >> 05_${meta.id}_FinalVersions.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":