From 705f904899e23157b6f25aa276af988b1842335d Mon Sep 17 00:00:00 2001 From: Carlos Gomes Date: Thu, 10 Jul 2025 17:20:09 -0300 Subject: [PATCH] up: modkit extract full using compression --- src/modules/modkit.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/modules/modkit.nf b/src/modules/modkit.nf index 16b98bc..d5a1a9d 100755 --- a/src/modules/modkit.nf +++ b/src/modules/modkit.nf @@ -13,7 +13,7 @@ process MODKIT { """ echo "starting modkit" ## Make Methylation TSV file - modkit extract full --queue-size 1000 -t 4 -i 10000 --mapped-only "${bam}" "${id}_modkit_output.tsv" + modkit extract full --bgzf --queue-size 1000 -t 4 -i 10000 --mapped-only "${bam}" "${id}_modkit_output.tsv" echo "extract successful" ## Make Methylation Table modkit pileup -t 4 -i 10000 --chunk-size 4 "${bam}" "${id}_modkit_pileup.bed" --log-filepath "${id}_modkit_pileup.log" -- GitLab