From 20b5797efc3bfecb255edac43edb5017a903e186 Mon Sep 17 00:00:00 2001 From: Mohammed Mahdi Date: Tue, 9 Jul 2024 15:02:34 +0900 Subject: [PATCH] updated customemodule for more multiqc output --- modules/local/custommodule.nf | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/modules/local/custommodule.nf b/modules/local/custommodule.nf index 0a03a8d..056fd85 100644 --- a/modules/local/custommodule.nf +++ b/modules/local/custommodule.nf @@ -20,6 +20,24 @@ process CUSTOMMODULE { script: def args = task.ext.args ?: '' """ + echo "# id: 'repeat summary'" > repeatmqc_mqc.tsv + echo "# section_name: 'repeat masking summary statistics'" >> repeatmqc_mqc.tsv + echo "# format: 'tsv'" >> repeatmqc_mqc.tsv + echo "# plot_type: 'bargraph'" >> repeatmqc_mqc.tsv + echo "# description: 'This plot shows a brief summary of each genomes whose repeats has been masked'" >> repeatmqc_mqc.tsv + echo "# pconfig:" >> repeatmqc_mqc.tsv + echo "# id: 'repeat summary'" >> repeatmqc_mqc.tsv + echo "# title: 'repeat summary'" >> repeatmqc_mqc.tsv + echo "# ylab: ''" >> repeatmqc_mqc.tsv + echo "id\tTotal scaffold length\tTotal contig length\ttantan masked bases\twindowmasker masked bases\trmodeler masked bases" >> repeatmqc_mqc.tsv + printf "\$(basename $assemt .assembly_summary)\t" >> repeatmqc_mqc.tsv + grep 'Total scaffold length' $assemt | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> repeatmqc_mqc.tsv + grep 'Total contig length' $assemt | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> repeatmqc_mqc.tsv + grep 'soft-masked bases' $assemt | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> repeatmqc_mqc.tsv + grep 'soft-masked bases' $assemw | tail -n 1 | awk '{print \$4}' | tr '\n' '\t' >> repeatmqc_mqc.tsv + grep 'soft-masked bases' $assemr | tail -n 1 | awk '{print \$4}' >> repeatmqc_mqc.tsv + + echo "# id: 'tantan repeat summary'" > tantanmqc_mqc.tsv echo "# section_name: 'tantan repeat masking summary statistics'" >> tantanmqc_mqc.tsv echo "# format: 'tsv'" >> tantanmqc_mqc.tsv