draft gather_sample_evidence.sh

Author: VJalili

src/bash_workflows/gather_sample_evidence.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# ./gather_sample_evidence.sh test NA12878.final.cram NA12878.final.cram.crai Homo_sapiens_assembly38.fasta Homo_sapiens_assembly38.fasta.fai Homo_sapiens_assembly38.dict primary_contigs.list preprocessed_intervals.interval_list
+
+set -Eeuo pipefail
+
+sample_id=${1}
+bam_or_cram_file=${2}
+bam_or_cram_index=${3}
+reference_fasta=${4}
+reference_index=${5}
+reference_dict=${6}
+primary_contigs_list=${7}
+preprocessed_intervals=${8}
+disabled_read_filters=${9:-"MappingQualityReadFilter"}
+collect_coverage=${10:-true}
+run_scramble=${11:-true}
+
+
+if [[ "${collect_coverage}" == true || "${run_scramble}" == true ]]; then
+  # Collects read counts at specified intervals.
+  # The count for each interval is calculated by counting the number of
+  # read starts that lie in the interval.
+  ./collect_counts.sh \
+    "${preprocessed_intervals}" \
+    "${bam_or_cram_file}" \
+    "${bam_or_cram_index}" \
+    "${sample_id}" \
+    "${reference_fasta}" \
+    "${reference_index}" \
+    "${reference_dict}" \
+    "/root/gatk.jar" \
+    "${disabled_read_filters}"
+fi
+

wdl/GatherSampleEvidence.wdl

@@ -179,6 +179,7 @@ workflow GatherSampleEvidence {
     }
   }
 
+  # ------------- done
   if (run_manta) {
     call manta.Manta {
       input:
@@ -243,6 +244,7 @@ workflow GatherSampleEvidence {
   }
 
   if (run_scramble) {
+    # condition not clear, it needs to run on this specific version only, or this and newer, or this and older?
     if (!defined(is_dragen_3_7_8)) {
       # check if the reads were aligned with dragen 3.7.8
       call CheckAligner {