nf-core · chris-cheshire · Jan 15, 2021 · Jan 15, 2021 · Jan 15, 2021 · Jan 15, 2021
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,29 @@ tests/
 testing/
 testing*
 *.pyc
+
+.local
+.config
+.bash_history
+
+R_sessionInfo.log
+
+dev/docker/static_reports/test_output/alignment_summary.csv
+dev/docker/static_reports/test_output/alignment_summary.png
+dev/docker/static_reports/test_output/report.pdf
+dev/docker/static_reports/test_output/log.txt
+dev/docker/static_reports/test_output/duplication_summary.csv
+
+dev/docker/static_reports/test_output/duplication_summary.png
+
+dev/docker/static_reports/test_output/frag_hist.csv
+
+dev/docker/static_reports/test_output/frag_hist.png
+
+dev/docker/static_reports/test_output/frag_violin.csv
+
+dev/docker/static_reports/test_output/frag_violin.png
+
+dev/docker/static_reports/test_data/tmp_dir/*
+
+dev/docker/static_reports/test_output/*
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+    "python.pythonPath": "/usr/local/Caskroom/miniconda/base/envs/cutrun/bin/python"
+}
diff --git a/assets/awk/bt2_report_to_csv.awk b/assets/awk/bt2_report_to_csv.awk
@@ -0,0 +1,35 @@
+#!/bin/awk -f
+
+# This awk script parses a bowtie2 alignment summary to a csv file for easier downstream processing
+
+BEGIN {
+    cols="bt2_total_reads:bt2_align1:bt2_align_gt1:bt2_non_aligned:bt2_total_aligned"
+    FS="\n"
+    RS="\n\n"
+    col_count=split(cols, col_arr, ":");
+    for(i=1; i<=col_count; i++) printf col_arr[i] ((i==col_count) ? "\n" : ",");
+}
+{
+   for (i=1; i<=NF; i++) {
+       if(index($i,"reads; of these:") != 0) {
+           split($i, line_split, " ");
+           data["bt2_total_reads"]=line_split[1];
+       }
+       if(index($i,"aligned concordantly exactly 1 time") != 0) {
+           split($i, line_split, " ");
+           data["bt2_align1"]=line_split[1];
+       }
+       if(index($i,"aligned concordantly >1 times") != 0) {
+           split($i, line_split, " ");
+           data["bt2_align_gt1"]=line_split[1];
+       }
+       if(index($i,"aligned concordantly 0 times") != 0) {
+           split($i, line_split, " ");
+           data["bt2_non_aligned"]=line_split[1];
+       }
+    }
+}
+END {
+    data["bt2_total_aligned"] = data["bt2_align1"] + data["bt2_align_gt1"]
+    for (i=1; i<=col_count; i++) printf data[col_arr[i]] ((i==col_count) ? "\n" : ",");
+} 
diff --git a/assets/awk/dt_frag_report_to_csv.awk b/assets/awk/dt_frag_report_to_csv.awk
@@ -0,0 +1,28 @@
+#!/bin/awk -f
+
+BEGIN {
+    cols="dt_frag_sampled:dt_frag_mean_len:dt_frag_min_len:dt_frag_max_len"
+    FS="\t"
+    RS="\n"
+    col_count=split(cols, col_arr, ":");
+    for(i=1; i<=col_count; i++) printf col_arr[i] ((i==col_count) ? "\n" : ",");
+}
+{
+    for (i=1; i<=NF; i++) {
+        if(index($i,"Frag. Sampled") !=0) {
+        data["dt_frag_sampled"]=i;
+        }
+        if(index($i,"Frag. Len. Mean") !=0) {
+        data["dt_frag_mean_len"]=i;
+        }
+        if(index($i,"Frag. Len. Min") !=0) {
+        data["dt_frag_min_len"]=i;
+        }
+        if(index($i,"Frag. Len. Max") !=0) {
+        data["dt_frag_max_len"]=i;
+        }    
+    }
+}
+END {
+    for (j=1; j<=col_count; j++) printf $(data[col_arr[j]]) ((j==col_count) ? "\n" : ",");    
+}