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"$" escaping typo fix
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Riley-Grindle committed Sep 11, 2024
1 parent 971e534 commit bdae2d0
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Showing 9 changed files with 13 additions and 13 deletions.
2 changes: 1 addition & 1 deletion modules/local/doubletfinder.nf
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Expand Up @@ -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}":
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10 changes: 5 additions & 5 deletions modules/local/feature_naming.nf
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Expand Up @@ -23,28 +23,28 @@ process FEATURE_NAMING {
"""
#!/bin/bash
gzcat ${sample_files}/features.tsv.gz | perl -ane 'if ($F[0] ne $F[1]) { print "$F[0]\t$F[1]::$F[0]\tExpression\n"; } else { print "$F[0]\t$F[1]\tExpression\n"; }' | gzip > features_new.tsv.gz
gzcat ${sample_files}/features.tsv.gz | perl -ane 'if (\$F[0] ne \$F[1]) { print "\$F[0]\t\$F[1]::\$F[0]\tExpression\n"; } else { print "\$F[0]\t\$F[1]\tExpression\n"; }' | gzip > features_new.tsv.gz
rm ${sample_files}/features.tsv.gz
mv features_new.tsv.gz ${sample_files}/features.tsv.gz
echo "MTgenes" > MT.csv
cut -f1 -d "," $gene_list | grep -v "^$" | tail -n +2 | perl -pe "s/^/\\t/;s/$/::/" > origMT.csv
cut -f1 -d "," $gene_list | grep -v "^\$" | tail -n +2 | perl -pe "s/^/\\t/;s/\$/::/" > origMT.csv
gzcat ${sample_files}/features.tsv.gz | grep -f origMT.csv | cut -f2 >> MT.csv
rm origMT.csv
echo "G2Mgenes" > G2M.csv
cut -f2 -d "," $gene_list | grep -v "^$" | tail -n +2 | perl -pe "s/^/\\t/;s/$/::/"> origG2M.csv
cut -f2 -d "," $gene_list | grep -v "^\$" | tail -n +2 | perl -pe "s/^/\\t/;s/\$/::/"> origG2M.csv
gzcat ${sample_files}/features.tsv.gz | grep -f origG2M.csv | cut -f2 >> G2M.csv
rm origG2M.csv
echo "Sgenes" > S.csv
cut -f3 -d "," $gene_list | grep -v "^$" | tail -n +2 | perl -pe "s/^/\\t/;s/$/::/"> origS.csv
cut -f3 -d "," $gene_list | grep -v "^\$" | tail -n +2 | perl -pe "s/^/\\t/;s/\$/::/"> origS.csv
gzcat ${sample_files}/features.tsv.gz | grep -f origS.csv | cut -f2 >> S.csv
rm origS.csv
echo "RMgenes" > RM.csv
cut -f4 -d "," $gene_list | grep -v "^$" | tail -n +2 | perl -pe "s/^/\\t/;s/$/::/"> origRM.csv
cut -f4 -d "," $gene_list | grep -v "^\$" | tail -n +2 | perl -pe "s/^/\\t/;s/\$/::/"> origRM.csv
gzcat ${sample_files}/features.tsv.gz | grep -f origRM.csv | cut -f2 >> RM.csv
rm UpdatedFiles/origRM.csv
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2 changes: 1 addition & 1 deletion modules/local/find_NN_clusters.nf
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Expand Up @@ -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}":
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2 changes: 1 addition & 1 deletion modules/local/integration.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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}":
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2 changes: 1 addition & 1 deletion modules/local/makeseurat.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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}":
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2 changes: 1 addition & 1 deletion modules/local/merge.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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}":
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2 changes: 1 addition & 1 deletion modules/local/normalize_qc.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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}":
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2 changes: 1 addition & 1 deletion modules/local/plotting.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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}":
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2 changes: 1 addition & 1 deletion modules/local/runpca.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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}":
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