peak_call.yaml 11 KB
Newer Older
aknecht2's avatar
aknecht2 committed
1
peak_call:
2
  - music[tool]:
3
4
5
    - narrow[peak_type]:
      - music_narrow:
          inputs:
aknecht2's avatar
aknecht2 committed
6
7
8
9
10
11
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
12
          outputs:
aknecht2's avatar
aknecht2 committed
13
14
15
16
17
18
19
20
21
            sorted_scale_129_all.bed:
              param_name: scale_129.bed
              final_result: true
            sorted_scale_194_all.bed:
              param_name: scale_194.bed
              final_result: true
            sorted_scale_291_all.bed:
              param_name: scale_291.bed
              final_result: true
22
23
24
    - punctate[peak_type]:
      - music_punctate:
          inputs:
aknecht2's avatar
aknecht2 committed
25
26
27
28
29
30
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
31
          outputs:
aknecht2's avatar
aknecht2 committed
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
            sorted_scale_129_all.bed:
              param_name: scale_129.bed
              final_result: true
            sorted_scale_194_all.bed:
              param_name: scale_194.bed
              final_result: true
            sorted_scale_291_all.bed:
              param_name: scale_291.bed
              final_result: true
            sorted_scale_437_all.bed:
              param_name: scale_437.bed
              final_result: true
            sorted_scale_656_all.bed:
              param_name: scale_656.bed
              final_result: true
            sorted_scale_985_all.bed:
              param_name: scale_985.bed
              final_result: true
            sorted_scale_1477_all.bed:
              param_name: scale_1477.bed
              final_result: true
            sorted_scale_2216_all.bed:
54
              param_name: scale_2216.bed
aknecht2's avatar
aknecht2 committed
55
              final_result: true
56
57
58
    - broad[peak_type]:
      - music_broad:
          inputs:
aknecht2's avatar
aknecht2 committed
59
60
61
62
63
64
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
65
          outputs:
aknecht2's avatar
aknecht2 committed
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
            sorted_scale_1459_all.bed:
              param_name: scale_1459.bed
              final_result: true
            sorted_scale_2189_all.bed:
              param_name: scale_2189.bed
              final_result: true
            sorted_scale_3284_all.bed:
              param_name: scale_3284.bed
              final_result: true
            sorted_scale_4926_all.bed:
              param_name: scale_4926.bed
              final_result: true
            sorted_scale_7389_all.bed:
              param_name: scale_7389.bed
              final_result: true
            sorted_scale_11084_all.bed:
              param_name: scale_11084.bed
              final_result: true
            sorted_scale_16626_all.bed:
              param_name: scale_16626.bed
              final_result: true
87
  - peakranger[tool]:
88
89
90
    - narrow[peak_type]:
      - peakranger_callpeak:
          inputs:
aknecht2's avatar
aknecht2 committed
91
92
93
94
95
96
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
97
          outputs:
aknecht2's avatar
aknecht2 committed
98
99
100
101
102
103
104
105
            region.bed:
              param_name: region_bed
            summit.bed:
              param_name: summit_bed
            details:
              param_name: details
            peakranger.log:
              param_name: log
106
107
      - peakranger_format_bed:
          inputs:
aknecht2's avatar
aknecht2 committed
108
109
            region.bed:
              param_name: result_peaks
110
          outputs:
aknecht2's avatar
aknecht2 committed
111
112
            region_sorted.bed:
              param_name: sorted_peaks
113
              final_result: true
114
115
      - peakranger_format_bed:
          inputs:
aknecht2's avatar
aknecht2 committed
116
117
            summit.bed:
              param_name: result_peaks
118
          outputs:
aknecht2's avatar
aknecht2 committed
119
120
            summit_sorted.bed:
              param_name: sorted_peaks
121
              final_result: true
122
  - ccat[tool]:
123
124
125
    - broad[peak_type]:
      - ccat_callpeak:
          inputs:
aknecht2's avatar
aknecht2 committed
126
127
128
129
130
131
132
133
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
            chrom.sizes:
              param_name: chrom.sizes
134
          outputs:
aknecht2's avatar
aknecht2 committed
135
136
137
138
139
140
141
142
143
144
145
146
            significant.peak:
              param_name: significant_peak
              prefix_join: "."
            significant.region:
              param_name: significant_region
              prefix_join: "."
            top100000.peak:
              param_name: top_100000_peak
              prefix_join: "."
            log:
              param_name: ccat_log
              prefix_join: "."
147
148
      - ccat_format_bed:
          inputs:
aknecht2's avatar
aknecht2 committed
149
150
            significant.region:
              param_name: result_peaks
151
          outputs:
aknecht2's avatar
aknecht2 committed
152
153
            region_sorted.bed:
              param_name: sorted_peaks
154
              final_result: true
155
156
      - ccat_format_bed:
          inputs:
aknecht2's avatar
aknecht2 committed
157
            significant.peak:
158
              param_name: result_peaks
159
          outputs:
aknecht2's avatar
aknecht2 committed
160
161
            peak_sorted.bed:
              param_name: sorted_peaks
162
              final_result: true
163
  - gem[tool]:
164
165
166
    - narrow[peak_type]:
      - gem_callpeak:
          inputs:
167
168
169
170
171
172
173
174
175
176
177
178
            prefix:
              param_name: prefix
            chrom.sizes:
              param_name: chrom.sizes
            signal.bed:
              param_name: signal.bed
            control.bed:
              param_name: control.bed
            genome_dir:
              param_name: genome
            chr_fasta:
              param_name: chr_fasta
179
          outputs:
180
181
182
183
184
185
            GEM_events.narrowPeak:
              param_name: gem_peak_result
              name_template: "$prefix$/$prefix$_GEM_events.narrowPeak"
            GPS_events.narrowPeak:
              param_name: gps_peak_result
              name_template: "$prefix$/$prefix$_GPS_events.narrowPeak"
186
187
      - sort_awk_sort_peaks:
          inputs:
188
            GEM_events.narrowPeak:
189
              param_name: result_peaks
190
          outputs:
191
192
193
            results_GEM_sorted.bed:
              param_name: sorted_peaks
              final_result: true
194
195
      - sort_awk_sort_peaks:
          inputs:
196
            GPS_events.narrowPeak:
197
              param_name: result_peaks
198
          outputs:
199
200
201
            results_GPS_sorted.bed:
              param_name: sorted_peaks
              final_result: true
aknecht2's avatar
aknecht2 committed
202
  - spp[tool]:
aknecht2's avatar
aknecht2 committed
203
    - cp:
aknecht2's avatar
aknecht2 committed
204
        inputs:
205
206
          signal.bed:
            param_name: input_file
207
        outputs:
208
209
          signal.tagAlign:
            param_name: output_file
aknecht2's avatar
aknecht2 committed
210
    - cp:
211
        inputs:
212
213
          control.bed:
            param_name: input_file
214
        outputs:
215
216
          control.tagAlign:
            param_name: output_file
217
218
219
    - narrow[peak_type]:
      - spp_nodups_narrow:
          inputs:
220
221
222
223
            signal.tagAlign:
              param_name: signal.tagAlign
            control.tagAlign:
              param_name: control.tagAlign
224
          outputs:
225
            results.narrowPeak.gz:
226
              param_name: result_peaks
227
            results.pdf:
228
              param_name: plots_pdf
229
230
            results.ccscore:
              param_name: score
231
232
      - sort_awk_sort_peaks:
          inputs:
233
            results.narrowPeak.gz:
234
              param_name: result_peaks
235
          outputs:
236
237
            results_sorted.bed:
              param_name: sorted_peaks
238
              final_result: true
239
240
241
    - broad[peak_type]:
      - spp_nodups_broad:
          inputs:
242
243
244
245
            signal.tagAlign:
              param_name: signal.tagAlign
            control.tagAlign:
              param_name: control.tagAlign
246
          outputs:
247
            results.broadPeak.gz:
248
              param_name: result_peaks
249
            results.pdf:
250
              param_name: plots_pdf
251
252
            results.ccscore:
              param_name: score
253
254
      - sort_awk_sort_peaks:
          inputs:
255
            results.broadPeak.gz:
256
              param_name: result_peaks
257
          outputs:
258
259
            results_sorted.bed:
              param_name: sorted_peaks
260
              final_result: true
aknecht2's avatar
aknecht2 committed
261
  - macs2[tool]:
262
263
264
    - narrow[peak_type]:
      - macs2_narrow:
          inputs:
265
266
267
268
269
270
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
271
          outputs:
272
273
274
            peaks.narrowPeak:
              param_name: result_peaks
            peaks.xls:
275
              param_name: result_excel
276
277
            summits.bed:
              param_name: result_summit
278
279
      - sort_awk_sort_peaks:
          inputs:
280
281
            peaks.narrowPeak:
              param_name: result_peaks
282
          outputs:
283
284
            results_sorted.bed:
              param_name: sorted_peaks
285
              final_result: true
286
287
288
    - broad[peak_type]:
      - macs2_broad:
          inputs:
289
290
291
292
293
294
            prefix:
              param_name: prefix
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
295
          outputs:
296
297
298
            peaks.broadPeak:
              param_name: result_peaks
            peaks.xls:
299
              param_name: result_excel
300
301
            summits.bed:
              param_name: result_summit
302
303
      - sort_awk_sort_peaks:
          inputs:
304
305
            peaks.broadPeak:
              param_name: result_peaks
306
          outputs:
307
308
            results_sorted.bed:
              param_name: sorted_peaks
309
              final_result: true
310
311
312
313
  - zerone[tool]:
    - broad[peak_type]:
      - zerone_callpeak:
          inputs:
314
315
316
317
            control.bam:
              param_name: control.bam
            signal.bam:
              param_name: signal.bam
318
          outputs:
319
320
321
            peaks.bed:
              param_name: result_peaks
      - zerone_format:
322
          inputs:
323
324
            peaks.bed:
              param_name: result_peaks
325
          outputs:
326
327
328
            results_sorted.bed:
              param_name: full_result
              final_result: true
329
330
331
332
  - hiddendomains[tool]:
    - broad[peak_type]:
      - hiddendomains_callpeak:
          inputs:
333
334
335
336
337
338
339
            control.bed:
              param_name: control.bed
            signal.bed:
              param_name: signal.bed
            chrom.sizes:
              param_name: chrom_sizes
            prefix:
340
              param_name: prefix
341
          outputs:
342
            analysis.bed:
343
344
345
346
347
348
349
350
351
352
              param_name: result_peaks
            vis.bed:
              param_name: enriched_bins
            domains.txt:
              param_name: domains
            control_bins.txt:
              param_name: control_bins
            treatment_bins.txt:
              param_name: treatment_bins
      - hiddendomains_format:
353
          inputs:
354
            analysis.bed:
355
              param_name: result_peaks
356
          outputs:
357
            results_sorted.bed:
358
              param_name: full_result
359
              final_result: true
360
  - pepr[tool]:
Natasha Pavlovikj's avatar
Natasha Pavlovikj committed
361
362
    - pepr_callpeak:
        inputs:
363
364
365
366
367
368
369
370
          control.bed:
            param_name: control.bed
          signal.bed:
            param_name: signal.bed
          prefix:
            param_name: prefix
          peak_type:
            param_name: peak_type
Natasha Pavlovikj's avatar
Natasha Pavlovikj committed
371
        outputs:
372
373
374
375
376
          results_sorted.bed:
            param_name: result_peaks
            final_result: true
          parameters.txt:
            param_name: pepr_params