tidying modules perl script to report versions

mdibl · Sep 11, 2024 · 6e4c2a5 · 6e4c2a5
1 parent bdae2d0
commit 6e4c2a5
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Showing 8 changed files with 8 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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}":