Merge branch 'master' into ct-add-bwa-depletion

broadinstitute · Jan 25, 2018 · 3a4dab9 · 3a4dab9
2 parents 0163510 + 67cc4b3
commit 3a4dab9
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Showing 3 changed files with 36 additions and 12 deletions.
diff --git a/pipes/WDL/workflows/align_and_plot.wdl b/pipes/WDL/workflows/align_and_plot.wdl
@@ -1,5 +1,8 @@
 import "tasks/reports.wdl" as reports
 
 workflow align_and_plot {
-  call reports.plot_coverage
+  call reports.plot_coverage {
+    input:
+      aligner_options = "-r Random -l 30 -g 40 -x 20 -t 502"
+  }
 }
diff --git a/pipes/WDL/workflows/tasks/assembly.wdl b/pipes/WDL/workflows/tasks/assembly.wdl
@@ -315,10 +315,24 @@ task refine_2x_and_plot {
     samtools flagstat ${sample_name}.bam | tee ${sample_name}.bam.flagstat.txt
     grep properly ${sample_name}.bam.flagstat.txt | cut -f 1 -d ' ' | tee read_pairs_aligned
     samtools view ${sample_name}.mapped.bam | cut -f10 | tr -d '\n' | wc -c | tee bases_aligned
-    expr $(cat bases_aligned) / $(cat assembly_length) | tee mean_coverage
+    echo $(( $(cat bases_aligned) / $(cat assembly_length) )) | tee mean_coverage
 
     # fastqc mapped bam
     reports.py fastqc ${sample_name}.mapped.bam ${sample_name}.mapped_fastqc.html
+
+    # plot coverage
+    if [ $(cat reads_aligned) != 0 ]; then
+      reports.py plot_coverage \
+        ${sample_name}.mapped.bam \
+        ${sample_name}.coverage_plot.pdf \
+        --plotFormat pdf \
+        --plotWidth 1100 \
+        --plotHeight 850 \
+        --plotDPI 100 \
+        --loglevel=DEBUG
+    else
+      touch ${sample_name}.coverage_plot.pdf ${sample_name}.mapped_fastqc.html
+    fi
   }
 
   output {

diff --git a/pipes/WDL/workflows/tasks/reports.wdl b/pipes/WDL/workflows/tasks/reports.wdl
@@ -43,24 +43,31 @@ task plot_coverage {
 
     samtools index ${sample_name}.mapped.bam
 
-    reports.py plot_coverage \
-      ${sample_name}.mapped.bam \
-      ${sample_name}.coverage_plot.pdf \
-      --plotFormat pdf \
-      --plotWidth 1100 \
-      --plotHeight 850 \
-      --plotDPI 100 \
-      --loglevel=DEBUG
-
     # collect figures of merit
     grep -v '^>' assembly.fasta | tr -d '\n' | wc -c | tee assembly_length
     grep -v '^>' assembly.fasta | tr -d '\nNn' | wc -c | tee assembly_length_unambiguous
     samtools view -c ${sample_name}.mapped.bam | tee reads_aligned
     samtools flagstat ${sample_name}.bam | tee ${sample_name}.bam.flagstat.txt
     grep properly ${sample_name}.bam.flagstat.txt | cut -f 1 -d ' ' | tee read_pairs_aligned
     samtools view ${sample_name}.mapped.bam | cut -f10 | tr -d '\n' | wc -c | tee bases_aligned
-    expr $(cat bases_aligned) / $(cat assembly_length) | tee mean_coverage
+    echo $(( $(cat bases_aligned) / $(cat assembly_length) )) | tee mean_coverage
+
+    # fastqc mapped bam
     reports.py fastqc ${sample_name}.mapped.bam ${sample_name}.mapped_fastqc.html
+
+    # plot coverage
+    if [ $(cat reads_aligned) != 0 ]; then
+      reports.py plot_coverage \
+        ${sample_name}.mapped.bam \
+        ${sample_name}.coverage_plot.pdf \
+        --plotFormat pdf \
+        --plotWidth 1100 \
+        --plotHeight 850 \
+        --plotDPI 100 \
+        --loglevel=DEBUG
+    else
+      touch ${sample_name}.coverage_plot.pdf ${sample_name}.mapped_fastqc.html
+    fi
   }
 
   output {