-
Notifications
You must be signed in to change notification settings - Fork 0
/
sc-multiome-filter.cwl
1715 lines (1515 loc) · 51.1 KB
/
sc-multiome-filter.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
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
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
cwlVersion: v1.0
class: CommandLineTool
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entryname: dummy_metadata.csv
entry: |
library_id
Experiment
- class: EnvVarRequirement
envDef:
R_MAX_VSIZE: $((inputs.vector_memory_limit * 1000000000).toString())
hints:
- class: DockerRequirement
dockerPull: biowardrobe2/sc-tools:v0.0.13
inputs:
feature_bc_matrices_folder:
type: Directory
inputBinding:
prefix: "--mex"
doc: |
Path to the folder with feature-barcode matrix from Cell Ranger ARC Count/Aggregate
experiment in MEX format. The rows consist of all the genes and peaks concatenated
together and the columns are restricted to those barcodes that are identified as cells.
aggregation_metadata:
type: File?
doc: |
Path to the metadata TSV/CSV file to set the datasets identities. If '--mex' points to
the Cell Ranger ARC Aggregate outputs, the aggr.csv file can be used. If input is not
provided, the default dummy_metadata.csv will be used instead.
atac_fragments_file:
type: File
secondaryFiles:
- .tbi
inputBinding:
prefix: "--fragments"
doc: |
Count and barcode information for every ATAC fragment observed in the experiment in TSV
format. Tbi-index file is required.
annotation_gtf_file:
type: File
inputBinding:
prefix: "--annotations"
doc: |
Path to the genome annotation file in GTF format.
grouping_data:
type: File?
inputBinding:
prefix: "--grouping"
doc: |
Path to the TSV/CSV file to define datasets grouping.
First column - 'library_id' with the values and order
that correspond to the 'library_id' column from the '
--identity' file, second column 'condition'.
Default: each dataset is assigned to its own group.
blacklist_regions_file:
type: File?
inputBinding:
prefix: "--blacklist"
doc: |
Path to the optional BED file with the genomic blacklist regions.
barcodes_data:
type: File?
inputBinding:
prefix: "--barcodes"
doc: |
Path to the TSV/CSV file to optionally prefilter and
extend Seurat object metadata be selected barcodes.
First column should be named as 'barcode'. If file
includes any other columns they will be added to the
Seurat object metadata ovewriting the existing ones if
those are present.
Default: all cells used, no extra metadata is added
rna_minimum_cells:
type: int?
inputBinding:
prefix: "--rnamincells"
doc: |
Include only genes detected in at least this many cells.
Default: 5 (applied to all datasets)
minimum_genes:
type:
- "null"
- int
- int[]
inputBinding:
prefix: "--mingenes"
doc: |
Include cells where at least this many genes are detected. If multiple values
provided, each of them will be applied to the correspondent dataset from the
'--mex' input based on the '--identity' file.
Default: 250 (applied to all datasets)
maximum_genes:
type:
- "null"
- int
- int[]
inputBinding:
prefix: "--maxgenes"
doc: |
Include cells with the number of genes not bigger than this value. If multiple
values provided, each of them will be applied to the correspondent dataset from
the '--mex' input based on the '--identity' file.
Default: 5000 (applied to all datasets)
rna_minimum_umi:
type:
- "null"
- int
- int[]
inputBinding:
prefix: "--rnaminumi"
doc: |
Include cells where at least this many UMI (RNA transcripts) are detected.
If multiple values provided, each of them will be applied to the correspondent
dataset from the '--mex' input based on the '--identity' file.
Default: 500 (applied to all datasets)
mito_pattern:
type: string?
inputBinding:
prefix: "--mitopattern"
doc: |
Regex pattern to identify mitochondrial genes.
Default: '^Mt-'
maximum_mito_perc:
type: float?
inputBinding:
prefix: "--maxmt"
doc: |
Include cells with the percentage of transcripts mapped to mitochondrial
genes not bigger than this value.
Default: 5 (applied to all datasets)
minimum_novelty_score:
type:
- "null"
- float
- float[]
inputBinding:
prefix: "--minnovelty"
doc: |
Include cells with the novelty score not lower than this value, calculated for
as log10(genes)/log10(UMI) for RNA assay. If multiple values provided, each of them will
be applied to the correspondent dataset from the '--mex' input based on the
'--identity' file.
Default: 0.8 (applied to all datasets)
atac_minimum_cells:
type: int?
inputBinding:
prefix: "--atacmincells"
doc: |
Include only peaks detected in at least this many cells.
Default: 5 (applied to all datasets)
atac_minimum_umi:
type:
- "null"
- int
- int[]
inputBinding:
prefix: "--atacminumi"
doc: |
Include cells where at least this many UMI (ATAC transcripts) are detected.
If multiple values provided, each of them will be applied to the correspondent
dataset from the '--mex' input based on the '--identity' file.
Default: 1000 (applied to all datasets)
maximum_nucl_signal:
type:
- "null"
- float
- float[]
inputBinding:
prefix: "--maxnuclsignal"
doc: |
Include cells with the nucleosome signal not bigger than this value.
Nucleosome signal quantifies the approximate ratio of mononucleosomal
to nucleosome-free fragments. If multiple values provided, each of
them will be applied to the correspondent dataset from the '--mex' input
based on the '--identity' file.
Default: 4 (applied to all datasets)
minimum_tss_enrich:
type:
- "null"
- float
- float[]
inputBinding:
prefix: "--mintssenrich"
doc: |
Include cells with the TSS enrichment score not lower than this value.
Score is calculated based on the ratio of fragments centered at the TSS
to fragments in TSS-flanking regions. If multiple values provided, each
of them will be applied to the correspondent dataset from the '--mex' input
based on the '--identity' file.
Default: 2 (applied to all datasets)
minimum_frip:
type:
- "null"
- float
- float[]
inputBinding:
prefix: "--minfrip"
doc: |
Include cells with the FRiP not lower than this value. If multiple values
provided, each of them will be applied to the correspondent dataset from the
'--mex' input based on the '--identity' file. FRiP is calculated for fragments.
Default: 0.15 (applied to all datasets)
maximum_blacklist_fraction:
type:
- "null"
- float
- float[]
inputBinding:
prefix: "--maxblacklist"
doc: |
Include cells with the fraction of fragments in
genomic blacklist regions not bigger than this value.
If multiple values provided, each of them will be
applied to the correspondent dataset from the '--mex'
input based on the '--identity' file.
Default: 0.05 (applied to all datasets)
call_by:
type: string?
inputBinding:
prefix: "--callby"
doc: |
Replace Cell Ranger ARC peaks with MACS2 peaks called
for cells grouped by the column from the optionally
provided --barcodes file. If --barcodes file was not
provided MACS2 peaks can be still called per dataset
by setting --callby to new.ident. Peaks are called
only after applying all RNA related thresholds,
maximum nucleosome signal, and minimum TSS enrichment
scores filters.
Default: do not call peaks
export_pdf_plots:
type: boolean?
inputBinding:
prefix: "--pdf"
doc: |
Export plots in PDF.
Default: false
color_theme:
type:
- "null"
- type: enum
symbols:
- "gray"
- "bw"
- "linedraw"
- "light"
- "dark"
- "minimal"
- "classic"
- "void"
inputBinding:
prefix: "--theme"
doc: |
Color theme for all generated plots. One of gray, bw, linedraw, light,
dark, minimal, classic, void.
Default: classic
verbose:
type: boolean?
inputBinding:
prefix: "--verbose"
doc: |
Print debug information.
Default: false
export_h5seurat_data:
type: boolean?
inputBinding:
prefix: "--h5seurat"
doc: |
Save Seurat data to h5seurat file.
Default: false
export_h5ad_data:
type: boolean?
inputBinding:
prefix: "--h5ad"
doc: |
Save Seurat data to h5ad file.
Default: false
output_prefix:
type: string?
inputBinding:
prefix: "--output"
doc: |
Output prefix.
Default: ./sc
parallel_memory_limit:
type: int?
inputBinding:
prefix: "--memory"
doc: |
Maximum memory in GB allowed to be shared between the workers
when using multiple --cpus.
Default: 32
vector_memory_limit:
type: int?
default: 128
doc: |
Maximum vector memory in GB allowed to be used by R.
Default: 128
threads:
type: int?
inputBinding:
prefix: "--cpus"
doc: |
Number of cores/cpus to use.
Default: 1
outputs:
raw_1_2_qc_mtrcs_pca_plot_png:
type: File?
outputBinding:
glob: "*_raw_1_2_qc_mtrcs_pca.png"
doc: |
PC1 and PC2 from the QC metrics PCA (not filtered).
PNG format
raw_1_2_qc_mtrcs_pca_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_1_2_qc_mtrcs_pca.pdf"
doc: |
PC1 and PC2 from the QC metrics PCA (not filtered).
PDF format
raw_2_3_qc_mtrcs_pca_plot_png:
type: File?
outputBinding:
glob: "*_raw_2_3_qc_mtrcs_pca.png"
doc: |
PC2 and PC3 from the QC metrics PCA (not filtered).
PNG format
raw_2_3_qc_mtrcs_pca_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_2_3_qc_mtrcs_pca.pdf"
doc: |
PC2 and PC3 from the QC metrics PCA (not filtered).
PDF format
raw_cells_count_plot_png:
type: File?
outputBinding:
glob: "*_raw_cells_count.png"
doc: |
Number of cells per dataset (not filtered).
PNG format
raw_cells_count_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_cells_count.pdf"
doc: |
Number of cells per dataset (not filtered).
PDF format
raw_rna_umi_dnst_plot_png:
type: File?
outputBinding:
glob: "*_raw_rna_umi_dnst.png"
doc: |
UMI per cell density for RNA assay (not filtered).
PNG format
raw_rna_umi_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_rna_umi_dnst.pdf"
doc: |
UMI per cell density for RNA assay (not filtered).
PDF format
raw_gene_dnst_plot_png:
type: File?
outputBinding:
glob: "*_raw_gene_dnst.png"
doc: |
Genes per cell density (not filtered).
PNG format
raw_gene_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_gene_dnst.pdf"
doc: |
Genes per cell density (not filtered).
PDF format
raw_gene_umi_corr_plot_png:
type: File?
outputBinding:
glob: "*_raw_gene_umi_corr.png"
doc: |
Genes vs UMI per cell correlation for RNA assay (not filtered).
PNG format
raw_gene_umi_corr_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_gene_umi_corr.pdf"
doc: |
Genes vs UMI per cell correlation for RNA assay (not filtered).
PDF format
raw_mito_dnst_plot_png:
type: File?
outputBinding:
glob: "*_raw_mito_dnst.png"
doc: |
Percentage of transcripts mapped to mitochondrial genes per cell density (not filtered).
PNG format
raw_mito_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_mito_dnst.pdf"
doc: |
Percentage of transcripts mapped to mitochondrial genes per cell density (not filtered).
PDF format
raw_nvlt_dnst_plot_png:
type: File?
outputBinding:
glob: "*_raw_nvlt_dnst.png"
doc: |
Novelty score per cell density for RNA assay (not filtered).
PNG format
raw_nvlt_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_nvlt_dnst.pdf"
doc: |
Novelty score per cell density for RNA assay (not filtered).
PDF format
raw_atac_umi_dnst_plot_png:
type: File?
outputBinding:
glob: "*_raw_atac_umi_dnst.png"
doc: |
UMI per cell density for ATAC assay (not filtered).
PNG format
raw_atac_umi_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_atac_umi_dnst.pdf"
doc: |
UMI per cell density for ATAC assay (not filtered).
PDF format
raw_peak_dnst_plot_png:
type: File?
outputBinding:
glob: "*_raw_peak_dnst.png"
doc: |
Peaks per cell density (not filtered).
PNG format
raw_peak_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_peak_dnst.pdf"
doc: |
Peaks per cell density (not filtered).
PDF format
raw_blck_dnst_plot_png:
type: File?
outputBinding:
glob: "*_raw_blck_dnst.png"
doc: |
Fraction of ATAC fragments within genomic blacklist regions per cell density (not filtered).
PNG format
raw_blck_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_blck_dnst.pdf"
doc: |
Fraction of ATAC fragments within genomic blacklist regions per cell density (not filtered).
PDF format
raw_rna_atac_umi_corr_plot_png:
type: File?
outputBinding:
glob: "*_raw_rna_atac_umi_corr.png"
doc: |
UMI per cell correlation for RNA vs ATAC assays (not filtered).
PNG format
raw_rna_atac_umi_corr_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_rna_atac_umi_corr.pdf"
doc: |
UMI per cell correlation for RNA vs ATAC assays (not filtered).
PDF format
raw_tss_atac_umi_corr_plot_png:
type: File?
outputBinding:
glob: "*_raw_tss_atac_umi_corr.png"
doc: |
TSS enrichment score vs UMI per cell correlation for ATAC assay (not filtered).
PNG format
raw_tss_atac_umi_corr_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_tss_atac_umi_corr.pdf"
doc: |
TSS enrichment score vs UMI per cell correlation for ATAC assay (not filtered).
PDF format
raw_qc_mtrcs_dnst_plot_png:
type: File?
outputBinding:
glob: "*_raw_qc_mtrcs_dnst.png"
doc: |
QC metrics per cell density (not filtered).
PNG format
raw_qc_mtrcs_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_qc_mtrcs_dnst.pdf"
doc: |
QC metrics per cell density (not filtered).
PDF format
raw_tss_nrch_plot_png:
type: File?
outputBinding:
glob: "*_raw_tss_nrch.png"
doc: |
TSS enrichment score (not filtered).
PNG format
raw_tss_nrch_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_tss_nrch.pdf"
doc: |
TSS enrichment score (not filtered).
PDF format
raw_frgm_hist_png:
type: File?
outputBinding:
glob: "*_raw_frgm_hist.png"
doc: |
Fragments length histogram (not filtered).
PNG format
raw_frgm_hist_pdf:
type: File?
outputBinding:
glob: "*_raw_frgm_hist.pdf"
doc: |
Fragments length histogram (not filtered).
PDF format
raw_rna_umi_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_raw_rna_umi_dnst_spl_cnd.png"
doc: |
Split by grouping condition UMI per cell density for RNA assay (not filtered).
PNG format
raw_rna_umi_dnst_spl_cnd_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_rna_umi_dnst_spl_cnd.pdf"
doc: |
Split by grouping condition UMI per cell density for RNA assay (not filtered).
PDF format
raw_gene_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_raw_gene_dnst_spl_cnd.png"
doc: |
Split by grouping condition genes per cell density (not filtered).
PNG format
raw_gene_dnst_spl_cnd_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_gene_dnst_spl_cnd.pdf"
doc: |
Split by grouping condition genes per cell density (not filtered).
PDF format
raw_mito_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_raw_mito_dnst_spl_cnd.png"
doc: |
Split by grouping condition the percentage of transcripts mapped
to mitochondrial genes per cell density (not filtered).
PNG format
raw_mito_dnst_spl_cnd_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_mito_dnst_spl_cnd.pdf"
doc: |
Split by grouping condition the percentage of transcripts mapped
to mitochondrial genes per cell density (not filtered).
PDF format
raw_nvlt_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_raw_nvlt_dnst_spl_cnd.png"
doc: |
Split by grouping condition the novelty score per cell density for RNA assay (not filtered).
PNG format
raw_nvlt_dnst_spl_cnd_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_nvlt_dnst_spl_cnd.pdf"
doc: |
Split by grouping condition the novelty score per cell density for RNA assay (not filtered).
PDF format
raw_atac_umi_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_raw_atac_umi_dnst_spl_cnd.png"
doc: |
Split by grouping condition UMI per cell density for ATAC assay (not filtered).
PNG format
raw_atac_umi_dnst_spl_cnd_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_atac_umi_dnst_spl_cnd.pdf"
doc: |
Split by grouping condition UMI per cell density for ATAC assay (not filtered).
PDF format
raw_peak_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_raw_peak_dnst_spl_cnd.png"
doc: |
Split by grouping condition peaks per cell density (not filtered).
PNG format
raw_peak_dnst_spl_cnd_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_peak_dnst_spl_cnd.pdf"
doc: |
Split by grouping condition peaks per cell density (not filtered).
PDF format
raw_blck_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_raw_blck_dnst_spl_cnd.png"
doc: |
Split by grouping condition the fraction of ATAC fragments within genomic
blacklist regions per cell density (not filtered).
PNG format
raw_blck_dnst_spl_cnd_plot_pdf:
type: File?
outputBinding:
glob: "*_raw_blck_dnst_spl_cnd.pdf"
doc: |
Split by grouping condition the fraction of ATAC fragments within genomic
blacklist regions per cell density (not filtered).
PDF format
mid_fltr_1_2_qc_mtrcs_pca_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_1_2_qc_mtrcs_pca.png"
doc: |
PC1 and PC2 from the QC metrics PCA (intermediate filtered).
PNG format
mid_fltr_1_2_qc_mtrcs_pca_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_1_2_qc_mtrcs_pca.pdf"
doc: |
PC1 and PC2 from the QC metrics PCA (intermediate filtered).
PDF format
mid_fltr_2_3_qc_mtrcs_pca_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_2_3_qc_mtrcs_pca.png"
doc: |
PC2 and PC3 from the QC metrics PCA (intermediate filtered).
PNG format
mid_fltr_2_3_qc_mtrcs_pca_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_2_3_qc_mtrcs_pca.pdf"
doc: |
PC2 and PC3 from the QC metrics PCA (intermediate filtered).
PDF format
mid_fltr_cells_count_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_cells_count.png"
doc: |
Number of cells per dataset (intermediate filtered).
PNG format
mid_fltr_cells_count_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_cells_count.pdf"
doc: |
Number of cells per dataset (intermediate filtered).
PDF format
mid_fltr_rna_umi_dnst_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_rna_umi_dnst.png"
doc: |
UMI per cell density for RNA assay (intermediate filtered).
PNG format
mid_fltr_rna_umi_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_rna_umi_dnst.pdf"
doc: |
UMI per cell density for RNA assay (intermediate filtered).
PDF format
mid_fltr_gene_dnst_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_gene_dnst.png"
doc: |
Genes per cell density (intermediate filtered).
PNG format
mid_fltr_gene_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_gene_dnst.pdf"
doc: |
Genes per cell density (intermediate filtered).
PDF format
mid_fltr_gene_umi_corr_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_gene_umi_corr.png"
doc: |
Genes vs UMI per cell correlation for RNA assay (intermediate filtered).
PNG format
mid_fltr_gene_umi_corr_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_gene_umi_corr.pdf"
doc: |
Genes vs UMI per cell correlation for RNA assay (intermediate filtered).
PDF format
mid_fltr_mito_dnst_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_mito_dnst.png"
doc: |
Percentage of transcripts mapped to mitochondrial genes per cell density (intermediate filtered).
PNG format
mid_fltr_mito_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_mito_dnst.pdf"
doc: |
Percentage of transcripts mapped to mitochondrial genes per cell density (intermediate filtered).
PDF format
mid_fltr_nvlt_dnst_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_nvlt_dnst.png"
doc: |
Novelty score per cell density for RNA assay (intermediate filtered).
PNG format
mid_fltr_nvlt_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_nvlt_dnst.pdf"
doc: |
Novelty score per cell density for RNA assay (intermediate filtered).
PDF format
mid_fltr_atac_umi_dnst_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_atac_umi_dnst.png"
doc: |
UMI per cell density for ATAC assay (intermediate filtered).
PNG format
mid_fltr_atac_umi_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_atac_umi_dnst.pdf"
doc: |
UMI per cell density for ATAC assay (intermediate filtered).
PDF format
mid_fltr_peak_dnst_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_peak_dnst.png"
doc: |
Peaks per cell density (intermediate filtered).
PNG format
mid_fltr_peak_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_peak_dnst.pdf"
doc: |
Peaks per cell density (intermediate filtered).
PDF format
mid_fltr_blck_dnst_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_blck_dnst.png"
doc: |
Fraction of ATAC fragments within genomic blacklist regions per cell density (intermediate filtered).
PNG format
mid_fltr_blck_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_blck_dnst.pdf"
doc: |
Fraction of ATAC fragments within genomic blacklist regions per cell density (intermediate filtered).
PDF format
mid_fltr_rna_atac_umi_corr_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_rna_atac_umi_corr.png"
doc: |
UMI per cell correlation for RNA vs ATAC assays (intermediate filtered).
PNG format
mid_fltr_rna_atac_umi_corr_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_rna_atac_umi_corr.pdf"
doc: |
UMI per cell correlation for RNA vs ATAC assays (intermediate filtered).
PDF format
mid_fltr_tss_atac_umi_corr_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_tss_atac_umi_corr.png"
doc: |
TSS enrichment score vs UMI per cell correlation for ATAC assay (intermediate filtered).
PNG format
mid_fltr_tss_atac_umi_corr_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_tss_atac_umi_corr.pdf"
doc: |
TSS enrichment score vs UMI per cell correlation for ATAC assay (intermediate filtered).
PDF format
mid_fltr_qc_mtrcs_dnst_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_qc_mtrcs_dnst.png"
doc: |
QC metrics per cell density (intermediate filtered).
PNG format
mid_fltr_qc_mtrcs_dnst_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_qc_mtrcs_dnst.pdf"
doc: |
QC metrics per cell density (intermediate filtered).
PDF format
mid_fltr_tss_nrch_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_tss_nrch.png"
doc: |
TSS enrichment score (intermediate filtered).
PNG format
mid_fltr_tss_nrch_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_tss_nrch.pdf"
doc: |
TSS enrichment score (intermediate filtered).
PDF format
mid_fltr_frgm_hist_png:
type: File?
outputBinding:
glob: "*_mid_fltr_frgm_hist.png"
doc: |
Fragments length histogram (intermediate filtered).
PNG format
mid_fltr_frgm_hist_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_frgm_hist.pdf"
doc: |
Fragments length histogram (intermediate filtered).
PDF format
mid_fltr_rna_umi_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_rna_umi_dnst_spl_cnd.png"
doc: |
Split by grouping condition UMI per cell density for RNA assay (intermediate filtered).
PNG format
mid_fltr_rna_umi_dnst_spl_cnd_plot_pdf:
type: File?
outputBinding:
glob: "*_mid_fltr_rna_umi_dnst_spl_cnd.pdf"
doc: |
Split by grouping condition UMI per cell density for RNA assay (intermediate filtered).
PDF format
mid_fltr_gene_dnst_spl_cnd_plot_png:
type: File?
outputBinding:
glob: "*_mid_fltr_gene_dnst_spl_cnd.png"
doc: |
Split by grouping condition genes per cell density (intermediate filtered).
PNG format
mid_fltr_gene_dnst_spl_cnd_plot_pdf: