diff --git a/main.nf b/main.nf index 4eb670dd200c2fab0198db5ed00a527339b62d7d..6dfd2f6501d49315b0cec9c2a91613cc8855f3ba 100644 --- a/main.nf +++ b/main.nf @@ -697,7 +697,7 @@ process remove_duplicates { mkdir -p stats/${sample} ## 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 echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat