-
Notifications
You must be signed in to change notification settings - Fork 28
/
Copy path.dockstore.yml
279 lines (279 loc) · 10.8 KB
/
.dockstore.yml
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
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
version: 1.2
workflows:
- name: align_and_count_multiple_report
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/align_and_count_multiple_report.wdl
- name: align_and_count
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/align_and_count.wdl
- name: align_and_plot
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/align_and_plot.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-align_and_plot-local.json
- name: assemble_denovo
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/assemble_denovo.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-assemble_denovo-local.json
- name: assemble_refbased
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/assemble_refbased.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-assemble_refbased-local.json
- name: augur_export_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_export_only.wdl
- name: augur_from_assemblies
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_assemblies.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-augur_from_assemblies-local.json
- name: augur_from_beast_mcc
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_beast_mcc.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-augur_from_beast_mcc-local.json
- name: augur_from_mltree
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_mltree.wdl
- name: augur_from_msa
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_msa.wdl
- name: augur_from_msa_with_subsampler
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/augur_from_msa_with_subsampler.wdl
- name: bams_multiqc
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/bams_multiqc.wdl
- name: beast_gpu
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/beast_gpu.wdl
- name: blastoff
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/blastoff.wdl
- name: chunk_blast
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/megablast_chunk.wdl
- name: classify_kaiju
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_kaiju.wdl
- name: classify_kraken2
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_kraken2.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-classify_kraken2-local.json
- name: classify_krakenuniq
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_krakenuniq.wdl
- name: classify_multi
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_multi.wdl
- name: classify_single
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_single.wdl
- name: contigs
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/contigs.wdl
- name: coverage_table
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/coverage_table.wdl
- name: create_enterics_qc_viz
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz.wdl
- name: create_enterics_qc_viz_general
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz_general.wdl
- name: demux_metag
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_metag.wdl
- name: demux_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_only.wdl
- name: demux_deplete
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_deplete.wdl
- name: demux_metadata_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_metadata_only.wdl
- name: demux_plus
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/demux_plus.wdl
- name: deplete_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/deplete_only.wdl
- name: detect_cross_contamination
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/detect_cross_contamination.wdl
testParameterFiles:
- name: detect_cross_contamination_precalled_vcfs
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/detect_cross_contamination_precalled_vcfs.wdl
- name: diff_genome_sets
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/diff_genome_sets.wdl
- name: downsample
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/downsample.wdl
- name: dump_gcloud_env_info
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/dump_gcloud_env_info.wdl
- name: fastq_to_ubam
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/fastq_to_ubam.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-fastq_to_ubam-local.json
- name: fetch_annotations
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/fetch_annotations.wdl
- name: fetch_sra_to_bam
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/fetch_sra_to_bam.wdl
- name: filter_classified_bam_to_taxa
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/filter_classified_bam_to_taxa.wdl
- name: filter_sequences
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/filter_sequences.wdl
- name: genbank_single
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/genbank_single.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-genbank_single-local.json
- name: isnvs_merge_to_vcf
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/isnvs_merge_to_vcf.wdl
- name: isnvs_lofreq
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/isnvs_lofreq.wdl
- name: isnvs_one_sample
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/isnvs_one_sample.wdl
- name: kraken2_build
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/kraken2_build.wdl
- name: mafft_and_snp
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_snp.wdl
- name: mafft_and_snp_annotated
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_snp_annotated.wdl
- name: mafft_and_trim
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/mafft_and_trim.wdl
- name: mafft
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/mafft.wdl
- name: merge_bams
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_bams.wdl
- name: merge_metagenomics
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_metagenomics.wdl
- name: merge_tar_chunks
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_tar_chunks.wdl
- name: merge_vcfs_and_annotate
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_vcfs_and_annotate.wdl
- name: merge_vcfs
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/merge_vcfs.wdl
- name: metagenomic_denovo
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/metagenomic_denovo.wdl
- name: multiqc_only
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/multiqc_only.wdl
- name: nextclade_single
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/nextclade_single.wdl
- name: populate_library_and_sample_tables_from_flowcell
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/populate_library_and_sample_tables_from_flowcell.wdl
- name: reconstruct_from_alignments
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/reconstruct_from_alignments.wdl
- name: sarscov2_batch_relineage
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_batch_relineage.wdl
- name: sarscov2_biosample_load
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_biosample_load.wdl
- name: sarscov2_data_release
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_data_release.wdl
- name: sarscov2_genbank
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_genbank.wdl
- name: sarscov2_genbank_ingest
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_genbank_ingest.wdl
- name: sarscov2_illumina_full
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_illumina_full.wdl
- name: sarscov2_lineages
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_lineages.wdl
testParameterFiles:
- /test/input/WDL/test_inputs-sarscov2_lineages-local.json
- name: calc_bam_read_depths
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/calc_bam_read_depths.wdl
- name: sarscov2_gisaid_ingest
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_gisaid_ingest.wdl
- name: sarscov2_nextclade_multi
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextclade_multi.wdl
- name: sarscov2_nextstrain
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextstrain.wdl
- name: sarscov2_nextstrain_aligned_input
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl
- name: sarscov2_sequencing_reports
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_sequencing_reports.wdl
- name: sarscov2_sra_to_genbank
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/sarscov2_sra_to_genbank.wdl
- name: scaffold_and_refine
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/scaffold_and_refine.wdl
- name: scaffold_and_refine_multitaxa
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/scaffold_and_refine_multitaxa.wdl
- name: subsample_by_casecounts
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_casecounts.wdl
- name: subsample_by_metadata
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_metadata.wdl
- name: subsample_by_metadata_with_focal
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/subsample_by_metadata_with_focal.wdl
- name: taxid_to_nextclade
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/taxid_to_nextclade.wdl
- name: terra_table_to_tsv
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/terra_table_to_tsv.wdl
- name: terra_tsv_to_table
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/terra_tsv_to_table.wdl
- name: terra_update_assemblies
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/terra_update_assemblies.wdl
- name: trimal
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/trimal.wdl
- name: classify_qiime2_multi
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/classify_qiime2_multi.wdl
- name: qiime_import_bam
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/bam_to_qiime.wdl
- name: unpack_archive_to_bucket
subclass: WDL
primaryDescriptorPath: /pipes/WDL/workflows/unpack_archive_to_bucket.wdl