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Unverified Commit b2bf20a4 authored by Nicolas Servant's avatar Nicolas Servant Committed by GitHub
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Update main.nf 


Co-authored-by: default avatarMatthias Hörtenhuber <mashehu@users.noreply.github.com>
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...@@ -697,7 +697,7 @@ process remove_duplicates { ...@@ -697,7 +697,7 @@ process remove_duplicates {
mkdir -p stats/${sample} mkdir -p stats/${sample}
## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs) ## Sort valid pairs and remove read pairs with same starts (i.e duplicated read pairs)
sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \ sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \\
awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat
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