-
Notifications
You must be signed in to change notification settings - Fork 4
/
rnaseq_pipeline_fastq.cwl
240 lines (220 loc) · 6.07 KB
/
rnaseq_pipeline_fastq.cwl
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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
#!/usr/bin/env cwl-runner
doc: |
TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/README.md).
Example input files: [Dockstore.json](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/rnaseq_pipeline_fastq-example.yml).
Quickstart instructions are [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/README.md#Quick Start).
[GitHub Repo](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL)
Pipeline steps:
1. Align RNA-seq reads with [STAR v2.5.3a](https://github.com/alexdobin/STAR).
2. Run [Picard](https://github.com/broadinstitute/picard) [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates).
2a. Create BAM index for MarkDuplicates BAM with [Samtools 1.6](https://github.com/samtools/samtools/releases) index.
3. Transcript quantification with [RSEM 1.3.0](https://deweylab.github.io/RSEM/)
4. Gene quantification and quality control with [RNA-SeQC 1.1.9](https://github.com/francois-a/rnaseqc)
cwlVersion: v1.0
class: Workflow
label: "TOPMed_RNA-seq"
requirements:
SubworkflowFeatureRequirement: {}
StepInputExpressionRequirement: {}
# hints:
# ResourceRequirement:
# coresMin: 4
# ramMin: 16
# #tmpdirMin: 51200
inputs:
star_index:
type: Directory
fastqs:
type: File[]
prefix_str:
type: string
rsem_ref_dir:
type: Directory
max_frag_len:
type: int
estimate_rspd:
type: boolean
is_stranded:
type: boolean
paired_end:
type: boolean
genes_gtf:
type: File
genome_fasta:
type: File
secondaryFiles:
- .fai
- ^.dict
rnaseqc_flags:
type: string[]
# gatk_flags:
# type:
# type: "null"
# type: array
# items: string
outputs:
star_output_bam:
outputSource: sort_bam/output_file
type: File
star_output_bam_index:
outputSource: index_bam/bam_index
type: File
star_output_transcriptome_bam:
outputSource: run_star/transcriptome_bam
type: File
star_output_chimeric_junctions:
outputSource: run_star/chimeric_junctions
type: File
star_output_chimeric_bam_file:
outputSource: sort_chimeras/output_file
type: File
star_output_chimeric_bam_index:
outputSource: index_chimeras/bam_index
type: File
star_output_read_counts:
outputSource: run_star/read_counts
type: File
star_output_junctions:
outputSource: run_star/junctions
type: File
star_output_junctions_pass1:
outputSource: run_star/junctions_pass1
type: File
star_output_logs:
outputSource: run_star/logs
type: File[]
markduplicates_output_bam:
outputSource: run_markduplicates/bam_file
type: File
markduplicates_output_metrics:
outputSource: run_markduplicates/metrics
type: File
markduplicates_bam_index:
outputSource: run_index_markduplicates_bam/bam_index
type: File
rsem_output_gene_results:
outputSource: run_rsem/gene_results
type: File
rsem_output_isoforms_results:
outputSource: run_rsem/isoforms_results
type: File
rna-seqc_output_gene_rpkm:
outputSource: run_rna-seqc/gene_rpkm
type: File
rna-seqc_output_gene_counts:
outputSource: run_rna-seqc/gene_counts
type: File
rna-seqc_output_exon_counts:
outputSource: run_rna-seqc/exon_counts
type: File
rna-seqc_output_count_metrics:
outputSource: run_rna-seqc/count_metrics
type: File
rna-seqc_output_count_outputs:
outputSource: run_rna-seqc/count_outputs
type: File
steps:
run_star:
run: star.cwl
in:
star_index: star_index
fastqs: fastqs
prefix: prefix_str
out:
[
bam,
transcriptome_bam,
chimeric_junctions,
chimeric_bam,
read_counts,
junctions,
junctions_pass1,
logs
]
sort_bam:
run: samtools-sort.cwl
in:
input:
source: run_star/bam
output_name:
source: prefix_str
valueFrom: $(self).Aligned.sortedByCoord.out.bam
out: [ output_file ]
sort_chimeras:
run: samtools-sort.cwl
in:
input:
source: run_star/chimeric_bam
output_name:
source: prefix_str
valueFrom: $(self).Chimeric.out.sorted.bam
out: [ output_file ]
index_bam:
run: indexbam.cwl
in:
input_bam: sort_bam/output_file
out: [bam_index]
index_chimeras:
run: indexbam.cwl
in:
input_bam: sort_chimeras/output_file
out: [bam_index]
run_markduplicates:
run: markduplicates.cwl
in:
input_bam: sort_bam/output_file
prefix_str: prefix_str
out:
[
bam_file,
metrics
]
run_index_markduplicates_bam:
run: indexbam.cwl
in:
input_bam: run_markduplicates/bam_file
out: [bam_index]
run_rsem:
run: rsem.cwl
in:
rsem_ref_dir: rsem_ref_dir
transcriptome_bam: run_star/transcriptome_bam
prefix_str: prefix_str
max_frag_len: max_frag_len
estimate_rspd: estimate_rspd
is_stranded: is_stranded
paired_end: paired_end
out:
[
gene_results,
isoforms_results
]
run_rna-seqc:
run: rna_seqc.cwl
in:
bam_file: run_index_markduplicates_bam/bam_index
genes_gtf: genes_gtf
genome_fasta: genome_fasta
prefix_str: prefix_str
rnaseqc_flags: rnaseqc_flags
# gatk_flags: gatk_flags
out:
[
gene_rpkm,
gene_counts,
exon_counts,
count_metrics,
count_outputs
]
$namespaces:
s: http://schema.org/
$schemas:
- http://dublincore.org/2012/06/14/dcterms.rdf
- http://xmlns.com/foaf/spec/20140114.rdf
- https://schema.org/docs/schema_org_rdfa.html
s:author:
- class: s:Person
s:id: https://orcid.org/0000-0003-3523-5312
s:email: christopherball@rti.org
s:name: Christopher Ball
s:codeRepository: https://github.com/heliumdatacommons/cwl_workflows