diff lumpy_wrapper.tcsh @ 0:e5150e64206a draft

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lumpy_wrapper.tcsh	Tue Oct 16 15:55:49 2018 -0400
@@ -0,0 +1,147 @@
+#!/bin/tcsh
+
+#USAGE:   lumpy_pipeline.tcsh PAIREDENDRUN OUTVCF    BAMS
+#EXAMPLE: lumpy_pipeline.tcsh 1            lumpy.vcf *.bam
+
+#PAIREDENDRUN - 1=paired end 0=single end
+#BAMS - Any bam files (will be sorted if not sorted & indexed if not indexed)
+
+#REQUIRED DEPENDENCIES:
+#lumpy
+#samtools
+#samblaster
+
+setenv PAIREDENDRUN `echo $argv | cut -f 1 -d " "`
+setenv OUTVCF       `echo $argv | cut -f 2 -d " "`
+setenv MYARGV       `echo $argv | cut -f 3-999 -d " "`
+
+setenv BAMS ''
+setenv SPLTS ''
+setenv DSCDS ''
+setenv SPLTOPTS ''
+
+foreach b ( $MYARGV )
+
+  echo
+  echo Preparing $b
+
+  echo
+  echo Parsing sample name
+  set SAMPLE=`echo $b | perl -e 'while(<>){s/\.bam//;print}'`
+
+  if ( $status ) then
+    echo "Unable to parse sample name in $b"
+    exit 1
+  endif
+
+  echo
+  echo "Checking BAM $b"
+  samtools view -H $b | perl -e '$y=0;while(<>){if(/SO:coordinate/){$y=1;}}if($y == 0){exit(2)}'
+  
+  if ( $status ) then
+    echo
+    echo "Sorting BAM $b"
+    samtools sort -o $b.sort -O BAM $b
+    if ( $status ) then
+      echo "Error sorting BAM $b"
+      exit 2
+    endif
+    mv -f $b.sort $b
+    if ( $status ) then
+      echo "Error renaming BAM $b.sort $b"
+      exit 3
+    endif
+  endif
+
+  perl -e 'unless(-e "$ARGV[0].bai"){exit(3)}' $b
+  if ( $status ) then
+    echo
+    echo "Indexing BAM $b"
+    samtools index -b $b
+    if ( $status ) then
+      echo "Error indexing BAM"
+      exit 4
+    endif
+  endif
+
+  echo
+  echo Getting splitters
+  samtools sort -n -O sam $b | samblaster -q -s /dev/stdout -o /dev/null | samtools view -Sb - | samtools sort - -o ${SAMPLE}.splitters.bam
+
+  if ( $status ) then
+    echo "Getting splitters from $b failed"
+    exit 5
+  endif
+
+  echo
+  echo Indexing splitters
+  samtools index -b ${SAMPLE}.splitters.bam
+
+  if ( $status ) then
+    echo "Indexing discordants in $b failed"
+    exit 6
+  endif
+
+  if ( $PAIREDENDRUN ) then
+    echo
+    echo Getting discordants
+    samtools view -b -F 1294 $b | samtools sort - -o ${SAMPLE}.discordants.bam
+
+    if ( $status ) then
+      echo "Getting discordants from $b failed"
+      exit 7
+    endif
+
+    echo
+    echo Indexing discordants
+    samtools index -b ${SAMPLE}.discordants.bam
+
+    if ( $status ) then
+      echo "Indexing discordants in $b failed"
+      exit 8
+    endif
+
+    if ( ${?DSCDS} > 0 && ${%DSCDS} > 0 )   setenv DSCDS "$DSCDS,${SAMPLE}.discordants.bam"
+    if ( ${?DSCDS} == 0 || ${%DSCDS} == 0 ) setenv DSCDS ${SAMPLE}.discordants.bam
+
+    if ( ${?SPLTS} > 0 && ${%SPLTS} > 0 )   setenv SPLTS "$SPLTS,${SAMPLE}.splitters.bam"
+    if ( ${?SPLTS} == 0 || ${%SPLTS} == 0 ) setenv SPLTS ${SAMPLE}.splitters.bam
+
+  else
+
+    if ( ${?SPLTOPTS} > 0 && ${%SPLTOPTS} > 0 )   setenv SPLTOPTS "$SPLTOPTS -sr id:${SAMPLE},bam_file:${SAMPLE}.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20"
+    if ( ${?SPLTOPTS} == 0 || ${%SPLTOPTS} == 0 ) setenv SPLTOPTS "-sr id:${SAMPLE},bam_file:${SAMPLE}.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20"
+
+  endif
+
+  if ( ${?BAMS} > 0 && ${%BAMS} > 0 )     setenv BAMS  "$BAMS,$b"
+  if ( ${?BAMS} == 0 || ${%BAMS} == 0 )   setenv BAMS  $b
+
+end
+
+if ( $PAIREDENDRUN ) then
+
+  echo
+  echo "Running: lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF"
+  lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF
+
+  if ( $status ) then
+    echo "lumpyexpress failed"
+    exit 9
+  endif
+
+else
+
+  echo
+  echo "Running lumpy: lumpy -mw 4 -tt 0 $SPLTOPTS > $OUTVCF"
+  lumpy -mw 4 -tt 0 $SPLTOPTS > $OUTVCF
+
+  if ( $status ) then
+    echo "lumpy failed"
+    exit 10
+  endif
+
+endif
+
+echo
+echo DONE