From 52bcfac9596485e12bd5f222bd54c99d53c872f8 Mon Sep 17 00:00:00 2001
From: Charles Plessy <charles.plessy@oist.jp>
Date: Thu, 18 Jul 2024 11:43:34 +0900
Subject: [PATCH] Combine two reports, plus minor changes.

---
 modules/local/custommodule.nf | 31 +++++++------------------------
 1 file changed, 7 insertions(+), 24 deletions(-)

diff --git a/modules/local/custommodule.nf b/modules/local/custommodule.nf
index d3345be..d8dee21 100644
--- a/modules/local/custommodule.nf
+++ b/modules/local/custommodule.nf
@@ -18,8 +18,8 @@ process CUSTOMMODULE {
     script:
     def args = task.ext.args ?: ''
     """
-    echo "# id: 'base content summary'" > gc_summary_mqc.tsv
-    echo "# section_name: 'base and contigs summary statistics'" >> gc_summary_mqc.tsv
+    echo "# id: 'base_content_summary'" > gc_summary_mqc.tsv
+    echo "# section_name: 'Base frequency'" >> gc_summary_mqc.tsv
     echo "# format: 'tsv'" >> gc_summary_mqc.tsv
     echo "# plot_type: 'bargraph'" >> gc_summary_mqc.tsv
     echo "# description: 'This plot shows a brief summary of each base content/percentage in the query genomes'" >> gc_summary_mqc.tsv
@@ -34,37 +34,20 @@ process CUSTOMMODULE {
         jq -r '[.contig_percent_a, .contig_percent_c, .contig_percent_g, .contig_percent_t, .contig_percent_n, .contig_non_acgtn] | @tsv' \$i >> gc_summary_mqc.tsv
     done
 
-    echo "# id: 'contigs length statistics'" > contig_length_mqc.tsv
-    echo "# section_name: 'base and contigs summary statistics'" >> contig_length_mqc.tsv
+    echo "# id: 'contigs_length_statistics'" > contig_length_mqc.tsv
+    echo "# section_name: 'Contig length statistics'" >> contig_length_mqc.tsv
     echo "# format: 'tsv'" >> contig_length_mqc.tsv
-    echo "# plot_type: 'heatmap'" >> contig_length_mqc.tsv
+    echo "# plot_type: 'table'" >> contig_length_mqc.tsv
     echo "# description: 'This plot shows a short statistics abouth the length of contigs in the query genomes'" >> contig_length_mqc.tsv
     echo "# pconfig:" >> contig_length_mqc.tsv
     echo "#    id: 'contigs length statistics'" >> contig_length_mqc.tsv
     echo "#    title: 'contigs length statistics'" >> contig_length_mqc.tsv
     echo "#    ylab: 'length'" >> contig_length_mqc.tsv
-    echo "id\tTOTALcontiglen\tMINcontiglen\tMAXcontiglen" >> contig_length_mqc.tsv
+    echo "id\tTOTALcontiglen\tMINcontiglen\tMAXcontiglen\ttotalcontigs\tcontigs>1k\tcontigs>10k" >> contig_length_mqc.tsv
     for i in $json
     do
         printf "\$(basename \$i .json)\t" >> contig_length_mqc.tsv
-        jq -r '[.total_contig_length, .min_contig_length, .max_contig_length] | @tsv' \$i >> contig_length_mqc.tsv
-    done
-
-    echo "# id: 'contigs number'" > contig_total_mqc.tsv
-    echo "# section_name: 'base and contigs summary statistics'" >> contig_total_mqc.tsv
-    echo "# format: 'tsv'" >> contig_total_mqc.tsv
-    echo "# plot_type: 'heatmap'" >> contig_total_mqc.tsv
-    echo "#    id: 'contigs length statistics'" >> contig_length_mqc.tsv
-    echo "# description: 'This plot shows the total number of contigs in each test with threshold length'" >> contig_total_mqc.tsv
-    echo "# pconfig:" >> contig_total_mqc.tsv
-    echo "#    id: 'number of contigs'" >> contig_total_mqc.tsv
-    echo "#    title: 'number of contigs'" >> contig_total_mqc.tsv
-    echo "#    ylab: 'number'" >> contig_total_mqc.tsv
-    echo "id\ttotalcontigs\tcontigs>1k\tcontigs>10k" >> contig_total_mqc.tsv
-    for i in $json
-    do
-        printf "\$(basename \$i .json)\t" >> contig_total_mqc.tsv
-        jq -r '[.total_contig, .contigs_greater_1k, .contigs_greater_10k] | @tsv' \$i >> contig_total_mqc.tsv
+        jq -r '[.total_contig_length, .min_contig_length, .max_contig_length, .total_contig, .contigs_greater_1k, .contigs_greater_10k] | @tsv' \$i >> contig_length_mqc.tsv
     done
     """
 }