Changeset 5838

Timestamp:

Feb 24, 2020, 3:45:46 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1218: Implement MIPs alignment

Added functions for the novoalign and merge steps.

File:

• other/pipeline/trunk/mips_functions.sh (modified) (1 diff)

other/pipeline/trunk/mips_functions.sh

@@ -192 +192 @@
 }
 
-
+# Align with novoalign 
+# Parameters:
+#   $1: Prefix of sample (used in output files)
+#   $2: Prefix for generated files (counter)
+# Global parameters:
+#   $NovoAlign: Path to novoalign exectable
+#   $NovoAlignOptions: Options for novoalign
+#   $NovoIndex: Path to index file 
+#   $AmpliconsBed: Path to amplicons BED file
+#   $NovoSort: Path to novosort executable
+#   $NumThreads: Number of threads to use
+#   $AlignedBams: For returning paths to aligned BAM files (used for input in the merge step)
+function novoalign {
+  local prefix=$1
+  local n=$2
+
+  if [ ! -f tmp/${n}.umi.bam ]; then
+    return
+  fi
+
+  ./stderrwrap.sh ${NovoAlign} \
+    -c ${NumThreads} \
+    ${NovoAlignOptions} \
+    -d ${NovoIndex} \
+    --tags MC,ZP \
+    -i PE ${min_insert}-${max_insert} \
+    --amplicons ${AmpliconsBed} \
+    1 out/${prefix}.novo_coverage.bed \
+    -f tmp/${n}.umi.bam \
+    > tmp/${n}.nosort.bam \
+    3> out/${prefix}.novo.log
+    
+  ./stderrwrap.sh ${NovoSort} \
+    -c ${NumThreads} -t . -i \
+    -o tmp/${n}.novo.bam \
+    tmp/${n}.nosort.bam \
+    3> tmp/${n}.sort.log
+
+  AlignedBams="${AlignedBams} -INPUT tmp/${n}.novo.bam"
+}
+
+# Merge BAM files
+# Global parameters:
+#   $AlignedBams: BAM files to merge (created by 'novoalign')
+function merge_bam {
+
+  ./stdwrap.sh ./picard2 MergeSamFiles \
+    -SORT_ORDER coordinate -ASSUME_SORTED true \
+    ${AlignedBams} \
+    -OUTPUT tmp/novo.bam \
+    > mergebam.out
+}
+