annotate lumpy_wrapper.tcsh @ 11:1adcc5678f70 draft default tip

planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 313a08616ebe4dea93d3e88d4e2a6f66ec920bf8
author hepcat72
date Fri, 24 May 2019 12:44:12 -0400
parents 48461adb2e6a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
1 #!/bin/tcsh
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
2
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
3 #USAGE: lumpy_pipeline.tcsh PAIREDENDRUN OUTVCF BAMS
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
4 #EXAMPLE: lumpy_pipeline.tcsh 1 lumpy.vcf *.bam
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
5
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
6 #PAIREDENDRUN - 1=paired end 0=single end
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
7 #BAMS - Any bam files (will be sorted if not sorted & indexed if not indexed)
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
8
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
9 #REQUIRED DEPENDENCIES:
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
10 #lumpy
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
11 #samtools
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
12 #samblaster
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
13
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
14 setenv PAIREDENDRUN `echo $argv | cut -f 1 -d " "`
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
15 setenv OUTVCF `echo $argv | cut -f 2 -d " "`
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
16 setenv MYARGV `echo $argv | cut -f 3-999 -d " "`
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
17
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
18 setenv BAMS ''
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
19 setenv SPLTS ''
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
20 setenv DSCDS ''
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
21 setenv SPLTOPTS ''
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
22
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
23 foreach b ( $MYARGV )
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
24
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
25 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
26 echo Preparing $b
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
27
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
28 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
29 echo Parsing sample name
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
30 set SAMPLE=`echo $b | perl -e 'while(<>){s/\.bam//;print}'`
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
31
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
32 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
33 echo "Unable to parse sample name in $b"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
34 exit 1
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
35 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
36
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
37 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
38 echo "Checking BAM $b"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
39 samtools view -H $b | perl -e '$y=0;while(<>){if(/SO:coordinate/){$y=1;}}if($y == 0){exit(2)}'
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
40
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
41 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
42 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
43 echo "Sorting BAM $b"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
44 samtools sort -o $b.sort -O BAM $b
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
45 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
46 echo "Error sorting BAM $b"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
47 exit 2
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
48 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
49 mv -f $b.sort $b
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
50 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
51 echo "Error renaming BAM $b.sort $b"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
52 exit 3
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
53 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
54 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
55
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
56 perl -e 'unless(-e "$ARGV[0].bai"){exit(3)}' $b
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
57 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
58 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
59 echo "Indexing BAM $b"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
60 samtools index -b $b
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
61 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
62 echo "Error indexing BAM"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
63 exit 4
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
64 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
65 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
66
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
67 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
68 echo Getting splitters
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
69 samtools sort -n -O sam $b | samblaster -q -s /dev/stdout -o /dev/null | samtools view -Sb - | samtools sort - -o ${SAMPLE}.splitters.bam
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
70
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
71 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
72 echo "Getting splitters from $b failed"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
73 exit 5
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
74 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
75
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
76 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
77 echo Indexing splitters
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
78 samtools index -b ${SAMPLE}.splitters.bam
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
79
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
80 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
81 echo "Indexing discordants in $b failed"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
82 exit 6
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
83 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
84
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
85 if ( $PAIREDENDRUN ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
86 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
87 echo Getting discordants
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
88 samtools view -b -F 1294 $b | samtools sort - -o ${SAMPLE}.discordants.bam
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
89
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
90 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
91 echo "Getting discordants from $b failed"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
92 exit 7
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
93 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
94
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
95 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
96 echo Indexing discordants
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
97 samtools index -b ${SAMPLE}.discordants.bam
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
98
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
99 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
100 echo "Indexing discordants in $b failed"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
101 exit 8
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
102 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
103
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
104 if ( ${?DSCDS} > 0 && ${%DSCDS} > 0 ) setenv DSCDS "$DSCDS,${SAMPLE}.discordants.bam"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
105 if ( ${?DSCDS} == 0 || ${%DSCDS} == 0 ) setenv DSCDS ${SAMPLE}.discordants.bam
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
106
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
107 if ( ${?SPLTS} > 0 && ${%SPLTS} > 0 ) setenv SPLTS "$SPLTS,${SAMPLE}.splitters.bam"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
108 if ( ${?SPLTS} == 0 || ${%SPLTS} == 0 ) setenv SPLTS ${SAMPLE}.splitters.bam
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
109
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
110 else
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
111
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
112 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"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
113 if ( ${?SPLTOPTS} == 0 || ${%SPLTOPTS} == 0 ) setenv SPLTOPTS "-sr id:${SAMPLE},bam_file:${SAMPLE}.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
114
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
115 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
116
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
117 if ( ${?BAMS} > 0 && ${%BAMS} > 0 ) setenv BAMS "$BAMS,$b"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
118 if ( ${?BAMS} == 0 || ${%BAMS} == 0 ) setenv BAMS $b
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
119
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
120 end
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
121
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
122 if ( $PAIREDENDRUN ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
123
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
124 echo
11
1adcc5678f70 planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 313a08616ebe4dea93d3e88d4e2a6f66ec920bf8
hepcat72
parents: 9
diff changeset
125 echo "Running: lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF"
1adcc5678f70 planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 313a08616ebe4dea93d3e88d4e2a6f66ec920bf8
hepcat72
parents: 9
diff changeset
126 lumpyexpress -B $BAMS -S $SPLTS -D $DSCDS -o $OUTVCF
0
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
127
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
128 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
129 echo "lumpyexpress failed"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
130 exit 9
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
131 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
132
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
133 else
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
134
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
135 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
136 echo "Running lumpy: lumpy -mw 4 -tt 0 $SPLTOPTS > $OUTVCF"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
137 lumpy -mw 4 -tt 0 $SPLTOPTS > $OUTVCF
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
138
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
139 if ( $status ) then
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
140 echo "lumpy failed"
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
141 exit 10
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
142 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
143
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
144 endif
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
145
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
146 echo
e5150e64206a planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
hepcat72
parents:
diff changeset
147 echo DONE