updated customemodule for more multiqc output

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