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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell.
6 Last modified June 28, 2016
7
8 Description: Decontaminates multiplexed assemblies via normalization and mapping.
9
10 Usage: decontaminate.sh reads=<file,file> ref=<file,file> out=<directory>
11 or
12 decontaminate.sh readnamefile=<file> refnamefile=<file> out=<directory>
13
14 Input Parameters:
15 reads=<file,file> Input reads, one file per library.
16 ref=<file,file> Input assemblies, one file per library.
17 readnamefile=<file> List of input reads, one line per library.
18 refnamefile=<file> List of input assemblies, one line per library.
19
20 interleaved=auto True forces paired/interleaved input; false forces single-ended mapping.
21 If not specified, interleaved status will be autodetected from read names.
22 unpigz=t Spawn a pigz (parallel gzip) process for faster decompression. Requires pigz to be installed.
23 touppercase=t (tuc) Convert lowercase letters in reads to upper case (otherwise they will not match the reference).
24
25 Output Parameters:
26 pigz=f Spawn a pigz (parallel gzip) process for faster compression. Requires pigz to be installed.
27 tmpdir=. Write temp files here. By default is uses the system's $TMPDIR or current directory.
28 outdir=. Write ouput files here.
29
30 Mapping Parameters:
31 kfilter=55 Set to a positive number N to require minimum N contiguous matches for a mapped read.
32 ambig=random Determines how coverage will be calculated for ambiguously-mapped reads.
33 first: Add coverage only at first genomic mapping location.
34 random: Add coverage at a random best-scoring location.
35 all: Add coverage at all best-scoring locations.
36 toss: Discard ambiguously-mapped reads without adding coverage.
37
38 Filtering Parameters:
39 minc=3.5 Min average coverage to retain scaffold.
40 minp=20 Min percent coverage to retain scaffold.
41 minr=18 Min mapped reads to retain scaffold.
42 minl=500 Min length to retain scaffold.
43 ratio=1.2 Contigs will not be removed by minc unless the coverage changed by at least this factor. 0 disables this filter.
44 mapraw=t Set true to map the unnormalized reads. Required to filter by 'ratio'.
45 basesundermin=-1 If positive, removes contigs with at least this many bases in low-coverage windows.
46 window=500 Sliding window size
47 windowcov=5 Average coverage below this will be classified as low.
48
49 Tadpole Parameters:
50 ecct=f Error-correct with Tadpole before normalization.
51 kt=42 Kmer length for Tadpole.
52 aggressive=f Do aggressive error correction.
53 conservative=f Do conservative error correction.
54 tadpoleprefilter=1 (tadpre) Ignore kmers under this depth to save memory.
55
56 Normalization Parameters:
57 mindepth=2 Min depth of reads to keep.
58 target=20 Target normalization depth.
59 hashes=4 Number of hashes in Bloom filter.
60 passes=1 Normalization passes.
61 minprob=0.5 Min probability of correctness to add a kmer.
62 dp=0.75 (depthpercentile) Percentile to use for depth proxy (0.5 means median).
63 prefilter=t Prefilter, for large datasets.
64 filterbits=32 (fbits) Bits per cell in primary filter.
65 prefilterbits=2 (pbits) Bits per cell in prefilter.
66 k=31 Kmer length for normalization. Longer is more precise but less sensitive.
67
68 Other parameters:
69 opfn=0 (onlyprocessfirstn) Set to a positive number to only process that many datasets. This is for internal testing of specificity.
70
71 Java Parameters:
72 -Xmx This will set Java's memory usage, overriding autodetection.
73 -Xmx20g will specify 20 gigs of RAM, and -Xmx800m will specify 800 megs.
74 The max is typically 85% of physical memory.
75 -eoom This flag will cause the process to exit if an
76 out-of-memory exception occurs. Requires Java 8u92+.
77 -da Disable assertions.
78
79 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
80 "
81 }
82
83 #This block allows symlinked shellscripts to correctly set classpath.
84 pushd . > /dev/null
85 DIR="${BASH_SOURCE[0]}"
86 while [ -h "$DIR" ]; do
87 cd "$(dirname "$DIR")"
88 DIR="$(readlink "$(basename "$DIR")")"
89 done
90 cd "$(dirname "$DIR")"
91 DIR="$(pwd)/"
92 popd > /dev/null
93
94 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
95 CP="$DIR""current/"
96 JNI="-Djava.library.path=""$DIR""jni/"
97 JNI=""
98
99 z="-Xmx1g"
100 z2="-Xms1g"
101 set=0
102
103 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
104 usage
105 exit
106 fi
107
108 calcXmx () {
109 source "$DIR""/calcmem.sh"
110 setEnvironment
111 parseXmx "$@"
112 if [[ $set == 1 ]]; then
113 return
114 fi
115 freeRam 15000m 84
116 z="-Xmx${RAM}m"
117 z2="-Xms${RAM}m"
118 }
119 calcXmx "$@"
120
121
122 decontaminate() {
123 local CMD="java $JNI $EA $EOOM $z $z2 -cp $CP jgi.DecontaminateByNormalization $@"
124 echo $CMD >&2
125 eval $CMD
126 }
127
128 decontaminate "$@"