/
manifest
178 lines (157 loc) · 8.73 KB
/
manifest
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
name=Trimmomatic
commandLine=<java> <java_flags> -jar <libdir>IlluminaFastqTrimmer.jar --threads=4 --input.file.1=<input.file.1> <input.file.2> --output.filename.base=<output.filename.base> --create.trimlog=<create.trimlog> --phred.encoding=<phred.encoding> <convert.phred.scores> <adapter.clip.sequence.file> <adapter.clip.seed.mismatches> <adapter.clip.palindrome.clip.threshold> <adapter.clip.simple.clip.threshold> <adapter.clip.min.length> <adapter.clip.keep.both.reads> <trim.leading.quality.threshold> <trim.trailing.quality.threshold> <max.info.target.length> <max.info.strictness> <sliding.window.size> <sliding.window.quality.threshold> <min.read.length> <extra.steps>
license=
taskDoc=doc.html
fileFormat=fq;fastq
taskType=RNA-seq
categories=RNA-seq;Preprocess & Utilities
quality=preproduction
os=any
privacy=public
description=Provides a variety of options for trimming Illumina FASTQ files of adapter sequences and low-quality reads.
version= updated convert phred scores value to preserve no convert option in pipelines
minGenePatternVersion=
author=Anthony Bolger et al, Usadel Lab, Rheinsch - Westfalische Technische Hochschule Aachen
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=The input FASTQ to be trimmed. For paired-end data, this should be the forward ("*_1" or "left") input file.
p1_fileFormat=fq;fastq;fq.gz;fastq.gz;fq.bz2;fastq.bz2
p1_name=input.file.1
p1_optional=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=
p2_MODE=IN
p2_TYPE=FILE
p2_default_value=
p2_description=The reverse ("*_2" or "right") input FASTQ of paired-end data to be trimmed.
p2_fileFormat=fq;fastq;fq.gz;fastq.gz;fq.bz2;fastq.bz2
p2_name=input.file.2
p2_optional=on
p2_prefix_when_specified=--input.file.2=
p2_type=java.io.File
p2_value=
p3_default_value=<input.file.1_basename>
p3_description=A base name to be used for the output files.
p3_name=output.filename.base
p3_optional=
p3_prefix_when_specified=
p3_type=java.lang.String
p4_MODE=IN
p4_TYPE=FILE
p4_choiceDir=ftp\://gpftp.broadinstitute.org/module_support_files/Trimmomatic_0.32/adapters
p4_choiceDirFilter=*.fa;*.fasta;*.FA;*.FASTA
p4_default_value=
p4_description=A FASTA file containing the adapter sequences, PCR sequences, etc. to be clipped. This parameter is required to enable adapter clipping. Files are provided for several Illumina pipelines but you can also provide your own; see the documentation for details. Be sure to choose a PE file for paired-end data and an SE file for single-end data.
p4_fileFormat=fa;fasta
p4_name=adapter.clip.sequence.file
p4_optional=on
p4_prefix_when_specified=--adapter.clip.sequence.file=
p4_type=java.io.File
p4_value=
p5_default_value=
p5_description=Specifies the maximum mismatch count which will still allow a full match to be performed. A value of 2 is recommended. This parameter is required to enable adapter clipping.
p5_name=adapter.clip.seed.mismatches
p5_optional=on
p5_prefix_when_specified=--adapter.clip.seed.mismatches=
p5_type=java.lang.Integer
p6_default_value=
p6_description=Specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment. This is the log10 probability against getting a match by random chance; values around 30 or more are recommended. This parameter is required to enable adapter clipping.
p6_name=adapter.clip.palindrome.clip.threshold
p6_optional=on
p6_prefix_when_specified=--adapter.clip.palindrome.clip.threshold=
p6_type=java.lang.Integer
p7_default_value=
p7_description=Specifies how accurate the match between any adapter etc. sequence must be against a read as a log10 probability against getting a match by random chance; values between 7-15 are recommended. This parameter is required to enable adapter clipping.
p7_name=adapter.clip.simple.clip.threshold
p7_optional=on
p7_prefix_when_specified=--adapter.clip.simple.clip.threshold=
p7_type=java.lang.Integer
p8_default_value=
p8_description=In addition to the alignment score, palindrome mode can verify that a minimum length of adapter has been detected. If unspecified, this defaults to 8 bases, for historical reasons. However, since palindrome mode has a very low false positive rate, this can be safely reduced, even down to 1, to allow shorter adapter fragments to be removed.
p8_name=adapter.clip.min.length
p8_optional=on
p8_prefix_when_specified=--adapter.clip.min.length=
p8_type=java.lang.Integer
p9_default_value=true
p9_description=Controls whether to keep both forward and reverse reads when trimming in palindrome mode. The reverse read is the same as the forward but in reverse complement and so carries no additional information. The default is "yes" (retain the reverse read) which is useful when downstream tools cannot handle a combination of paired and unpaired reads.
p9_name=adapter.clip.keep.both.reads
p9_optional=
p9_prefix_when_specified=--adapter.clip.keep.both.reads=
p9_type=java.lang.String
p9_value=true\=yes;false\=no
p10_default_value=
p10_description=Remove low quality bases from the beginning. As long as a base has a value below this threshold the base is removed and the next base will be investigated.
p10_name=trim.leading.quality.threshold
p10_optional=on
p10_prefix_when_specified=--trim.leading.quality.threshold=
p10_type=java.lang.Integer
p11_default_value=
p11_description=Remove low quality bases from the end. As long as a base has a value below this threshold the base is removed and the next trailing base will be investigated.
p11_name=trim.trailing.quality.threshold
p11_optional=on
p11_prefix_when_specified=--trim.trailing.quality.threshold=
p11_type=java.lang.Integer
p12_default_value=
p12_description=Performs a Max Info adaptive quality trim, balancing the benefits of retaining longer reads against the costs of retaining bases with errors. This parameter specifies the read length which is likely to allow the location of the read within the target sequence to be determined.
p12_name=max.info.target.length
p12_optional=on
p12_prefix_when_specified=--max.info.target.length=
p12_type=java.lang.Integer
p13_default_value=
p13_description=This value, which should be set between 0 and 1, specifies the balance between preserving as much read length as possible vs. removal of incorrect bases. A low value of this parameter (<0.2) favors longer reads, while a high value (>0.8) favors read correctness. Both max.info.target.length and max.info.strictness are required for the Max Info quality trim.
p13_name=max.info.strictness
p13_optional=on
p13_prefix_when_specified=--max.info.strictness=
p13_type=java.lang.Integer
p14_default_value=
p14_description=Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold. By considering multiple bases, a single poor quality base will not cause the removal of high quality data later in the read. This parameter specifies the number of bases to average across.
p14_name=sliding.window.size
p14_optional=on
p14_prefix_when_specified=--sliding.window.size=
p14_type=java.lang.Integer
p15_default_value=
p15_description=Specifies the average quality required for the sliding window trimming. Both sliding.window.size and sliding.window.quality.threshold are required to enable the sliding window trimming.
p15_name=sliding.window.quality.threshold
p15_optional=on
p15_prefix_when_specified=--sliding.window.quality.threshold=
p15_type=java.lang.Integer
p16_default_value=
p16_description=Remove reads that fall below the specified minimal length.
p16_name=min.read.length
p16_optional=on
p16_prefix_when_specified=--min.read.length=
p16_type=java.lang.Integer
p17_default_value=
p17_description=Extra steps to be performed after any other processing. These must be specified in exactly the format described in the Trimmomatic manual; see the documentation for details. This is recommended for advanced users only.
p17_name=extra.steps
p17_optional=on
p17_prefix_when_specified=--extra.steps=
p17_type=java.lang.String
p18_default_value=phred33
p18_description=Allows you to specify the phred quality encoding. The default is phred33, which matches modern Illumina pipelines.
p18_fileFormat=
p18_name=phred.encoding
p18_optional=
p18_prefix_when_specified=
p18_type=java.lang.String
p18_value=phred33;phred64
p19_default_value=
p19_description=Convert phred scores into a particular encoding. Leave this blank for no conversion.
p19_fileFormat=
p19_name=convert.phred.scores
p19_optional=on
p19_prefix_when_specified=--convert.phred.scores=
p19_type=java.lang.String
p19_value=\=no conversion;to_phred33\=To phred33;to_phred64\=To phred64
p20_default_value=false
p20_description=Create a log of the trimming process. This gives details on what operations were performed, etc. but can be quite lengthy.
p20_fileFormat=
p20_name=create.trimlog
p20_optional=
p20_prefix_when_specified=
p20_type=java.lang.String
p20_value=true\=yes;false\=no
requiredPatchLSIDs=
requiredPatchURLs=