Skip to content

Commit d9bbc74

Browse files
rhshahrhshah
committed
Merge branch 'release/1.2.4'
2 parents 18a44c5 + a493b7f commit d9bbc74

File tree

9 files changed

+727
-57
lines changed

9 files changed

+727
-57
lines changed

‎command_line_tools‎

‎qc_duplex_bam/qc_duplex_bam_v2.0.cwl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -381,7 +381,7 @@ steps:
381381
- id: sequence_qc_noise_n
382382
- id: sequence_qc_noise_del
383383
- id: sequence_qc_figures
384-
run: ../command_line_tools/sequence_qc/0.2.3/sequence_qc_0.2.3.cwl
384+
run: ../command_line_tools/sequence_qc/0.2.4/sequence_qc_0.2.4.cwl
385385
'sbg:x': 353.515625
386386
'sbg:y': 1426.328125
387387
- id: biometrics_extract_0_2_14

‎qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl‎

Lines changed: 21 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -2140,13 +2140,13 @@
21402140
},
21412141
{
21422142
"class": "CommandLineTool",
2143-
"id": "#sequence_qc_0.2.3.cwl",
2143+
"id": "#sequence_qc_0.2.4.cwl",
21442144
"baseCommand": [
21452145
"calculate_noise"
21462146
],
21472147
"inputs": [
21482148
{
2149-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/reference",
2149+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/reference",
21502150
"type": "File",
21512151
"inputBinding": {
21522152
"position": 0,
@@ -2158,7 +2158,7 @@
21582158
"doc": "Path to reference fasta, containing all regions in bed_file"
21592159
},
21602160
{
2161-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/bam_file",
2161+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/bam_file",
21622162
"type": "File",
21632163
"inputBinding": {
21642164
"position": 0,
@@ -2170,7 +2170,7 @@
21702170
"doc": "Path to BAM file for calculating noise [required]"
21712171
},
21722172
{
2173-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/bed_file",
2173+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/bed_file",
21742174
"type": "File",
21752175
"inputBinding": {
21762176
"position": 0,
@@ -2179,7 +2179,7 @@
21792179
"doc": "Path to BED file containing regions over which to calculate noise [required]"
21802180
},
21812181
{
2182-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sample_id",
2182+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sample_id",
21832183
"type": "string",
21842184
"inputBinding": {
21852185
"position": 0,
@@ -2188,7 +2188,7 @@
21882188
"doc": "Prefix to include in all output file names"
21892189
},
21902190
{
2191-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/threshold",
2191+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/threshold",
21922192
"type": [
21932193
"null",
21942194
"float"
@@ -2200,7 +2200,7 @@
22002200
"doc": "Alt allele frequency past which to ignore positions from the calculation."
22012201
},
22022202
{
2203-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/truncate",
2203+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/truncate",
22042204
"type": [
22052205
"null",
22062206
"int"
@@ -2212,7 +2212,7 @@
22122212
"doc": "Whether to exclude trailing bases from reads that only partially overlap the bed file (0 or 1)"
22132213
},
22142214
{
2215-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/min_mapq",
2215+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/min_mapq",
22162216
"type": [
22172217
"null",
22182218
"int"
@@ -2224,7 +2224,7 @@
22242224
"doc": "Exclude reads with a lower mapping quality"
22252225
},
22262226
{
2227-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/min_basq",
2227+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/min_basq",
22282228
"type": [
22292229
"null",
22302230
"int"
@@ -2238,49 +2238,49 @@
22382238
],
22392239
"outputs": [
22402240
{
2241-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_pileup",
2241+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_pileup",
22422242
"type": "File",
22432243
"outputBinding": {
22442244
"glob": "${\n return inputs.sample_id + '_pileup.tsv'\n}"
22452245
}
22462246
},
22472247
{
2248-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_positions",
2248+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_positions",
22492249
"type": "File",
22502250
"outputBinding": {
22512251
"glob": "${\n return inputs.sample_id + '_noise_positions.tsv'\n}"
22522252
}
22532253
},
22542254
{
2255-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_by_substitution",
2255+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_by_substitution",
22562256
"type": "File",
22572257
"outputBinding": {
22582258
"glob": "${\n return inputs.sample_id + '_noise_by_substitution.tsv'\n}"
22592259
}
22602260
},
22612261
{
2262-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_acgt",
2262+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_acgt",
22632263
"type": "File",
22642264
"outputBinding": {
22652265
"glob": "${\n return inputs.sample_id + '_noise_acgt.tsv'\n}"
22662266
}
22672267
},
22682268
{
2269-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_n",
2269+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_n",
22702270
"type": "File",
22712271
"outputBinding": {
22722272
"glob": "${\n return inputs.sample_id + '_noise_n.tsv'\n}"
22732273
}
22742274
},
22752275
{
2276-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_noise_del",
2276+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_noise_del",
22772277
"type": "File",
22782278
"outputBinding": {
22792279
"glob": "${\n return inputs.sample_id + '_noise_del.tsv'\n}"
22802280
}
22812281
},
22822282
{
2283-
"id": "#sequence_qc_0.2.3.cwl/calculate_noise_0_2_3/sequence_qc_figures",
2283+
"id": "#sequence_qc_0.2.4.cwl/calculate_noise_0_2_4/sequence_qc_figures",
22842284
"type": "File",
22852285
"outputBinding": {
22862286
"glob": "${\n return inputs.sample_id + '_noise.html'\n}"
@@ -2295,7 +2295,7 @@
22952295
},
22962296
{
22972297
"class": "DockerRequirement",
2298-
"dockerPull": "ghcr.io/msk-access/sequence_qc:0.2.3"
2298+
"dockerPull": "ghcr.io/msk-access/sequence_qc:0.2.4"
22992299
},
23002300
{
23012301
"class": "InlineJavascriptRequirement"
@@ -2320,8 +2320,8 @@
23202320
"http://xmlns.com/foaf/0.1/member": [
23212321
{
23222322
"class": "http://xmlns.com/foaf/0.1/Person",
2323-
"http://xmlns.com/foaf/0.1/mbox": "mailto:murphyc4@mskcc.org",
2324-
"http://xmlns.com/foaf/0.1/name": "Charlie Murphy"
2323+
"http://xmlns.com/foaf/0.1/mbox": "mailto:shahr2@mskcc.org",
2324+
"http://xmlns.com/foaf/0.1/name": "Ronak Shah"
23252325
}
23262326
],
23272327
"http://xmlns.com/foaf/0.1/name": "Memorial Sloan Kettering Cancer Center"
@@ -2344,7 +2344,7 @@
23442344
{
23452345
"class": "http://usefulinc.com/ns/doap#Version",
23462346
"http://usefulinc.com/ns/doap#name": "sesquence_qc",
2347-
"http://usefulinc.com/ns/doap#revision": "0.2.3"
2347+
"http://usefulinc.com/ns/doap#revision": "0.2.4"
23482348
}
23492349
]
23502350
},
@@ -3031,7 +3031,7 @@
30313031
"id": "#main/calculate_noise/sequence_qc_figures"
30323032
}
30333033
],
3034-
"run": "#sequence_qc_0.2.3.cwl",
3034+
"run": "#sequence_qc_0.2.4.cwl",
30353035
"https://www.sevenbridges.com/x": 353.515625,
30363036
"https://www.sevenbridges.com/y": 1426.328125
30373037
},

‎vardict_workflow/run_processed_vardict.cwl‎

Lines changed: 20 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -59,6 +59,24 @@ outputs:
5959
type: File
6060
'sbg:x': 1064.255126953125
6161
'sbg:y': 213.53125
62+
- id: vardict_output
63+
outputSource:
64+
- vardict/output
65+
type: File
66+
'sbg:x': 397.9921875
67+
'sbg:y': 590.5
68+
- id: single_filter_vcf
69+
outputSource:
70+
- pv_vardict_single_filter/vcf
71+
type: File
72+
'sbg:x': 688.9921875
73+
'sbg:y': 587.5
74+
- id: single_filter_vcf_complex
75+
outputSource:
76+
- pv_vardict_single_filter/vcf_complex
77+
type: File
78+
'sbg:x': 942.9921875
79+
'sbg:y': 552.5
6280
steps:
6381
- id: vardict
6482
in:
@@ -113,8 +131,8 @@ steps:
113131
- id: vcf
114132
run: >-
115133
../command_line_tools/postprocessing_variant_calls/0.1.5/pv_vardict_single_filter.cwl
116-
'sbg:x': 513.37158203125
117-
'sbg:y': 213.53125
134+
'sbg:x': 483
135+
'sbg:y': 220
118136
- id: variants_concat
119137
in:
120138
- id: fastaRef

‎vardict_workflow/run_processed_vardict__packed.cwl‎

Lines changed: 29 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1731,6 +1731,33 @@
17311731
"type": "File",
17321732
"https://www.sevenbridges.com/x": 1064.255126953125,
17331733
"https://www.sevenbridges.com/y": 213.53125
1734+
},
1735+
{
1736+
"id": "#main/vardict_output",
1737+
"outputSource": [
1738+
"#main/vardict/output"
1739+
],
1740+
"type": "File",
1741+
"https://www.sevenbridges.com/x": 397.9921875,
1742+
"https://www.sevenbridges.com/y": 590.5
1743+
},
1744+
{
1745+
"id": "#main/single_filter_vcf",
1746+
"outputSource": [
1747+
"#main/pv_vardict_single_filter/vcf"
1748+
],
1749+
"type": "File",
1750+
"https://www.sevenbridges.com/x": 688.9921875,
1751+
"https://www.sevenbridges.com/y": 587.5
1752+
},
1753+
{
1754+
"id": "#main/single_filter_vcf_complex",
1755+
"outputSource": [
1756+
"#main/pv_vardict_single_filter/vcf_complex"
1757+
],
1758+
"type": "File",
1759+
"https://www.sevenbridges.com/x": 942.9921875,
1760+
"https://www.sevenbridges.com/y": 552.5
17341761
}
17351762
],
17361763
"steps": [
@@ -1837,8 +1864,8 @@
18371864
}
18381865
],
18391866
"run": "#pv_vardict_single_filter.cwl",
1840-
"https://www.sevenbridges.com/x": 513.37158203125,
1841-
"https://www.sevenbridges.com/y": 213.53125
1867+
"https://www.sevenbridges.com/x": 483,
1868+
"https://www.sevenbridges.com/y": 220
18421869
},
18431870
{
18441871
"id": "#main/variants_concat",

‎variant_annotation/README.md‎

Lines changed: 22 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -6,16 +6,25 @@
66

77
- [snpift](https://msk-access.gitbook.io/command-line-tools-cwl/snpsift_annotate_5.0/)
88
- [vcf2maf](https://msk-access.gitbook.io/command-line-tools-cwl/vcf2maf_1.6.21/)
9+
- [maf_annotated_by_bed](https://msk-access.gitbook.io/command-line-tools-cwl/postprocessing_variant_calls/0.2.0/maf_annotated_by_bed/)
910

1011
#### Usage
1112

1213
```bash
13-
usage: variant_annotation.cwl [-h] --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF
14+
usage: variant_annotation.cwl
15+
[-h] --input_cosmicCountDB_vcf INPUT_COSMICCOUNTDB_VCF
1416
--vardict_input_vcf VARDICT_INPUT_VCF --input_cosmicprevalenceDB_vcf
1517
INPUT_COSMICPREVALENCEDB_VCF [--min_hom_vaf MIN_HOM_VAF]
16-
[--output_mafName OUTPUT_MAFNAME] [--retain_info RETAIN_INFO]
18+
[--output_vcf2mafName OUTPUT_VCF2MAFNAME] [--retain_info RETAIN_INFO]
1719
[--tumor_id TUMOR_ID] [--snpsift_countOpName SNPSIFT_COUNTOPNAME]
18-
[--snpsift_prevalOpName SNPSIFT_PREVALOPNAME]
20+
[--snpsift_prevalOpName SNPSIFT_PREVALOPNAME] --opOncoKbMafName
21+
OPONCOKBMAFNAME --oncoKbApiToken ONCOKBAPITOKEN
22+
[--oncoKbAnnotateHotspots] --input_complexity_bed INPUT_COMPLEXITY_BED
23+
--input_DUST_bed INPUT_DUST_BED
24+
[--output_DUST_filename OUTPUT_DUST_FILENAME]
25+
[--column_name_DUST COLUMN_NAME_DUST]
26+
[--output_complexity_filename OUTPUT_COMPLEXITY_FILENAME]
27+
[--column_name_complexity COLUMN_NAME_COMPLEXITY]
1928
[job_order]
2029

2130
positional arguments:
@@ -27,10 +36,19 @@ optional arguments:
2736
--vardict_input_vcf VARDICT_INPUT_VCF
2837
--input_cosmicprevalenceDB_vcf INPUT_COSMICPREVALENCEDB_VCF
2938
--min_hom_vaf MIN_HOM_VAF
30-
--output_mafName OUTPUT_MAFNAME
39+
--output_vcf2mafName OUTPUT_VCF2MAFNAME
3140
--retain_info RETAIN_INFO
3241
--tumor_id TUMOR_ID
3342
--snpsift_countOpName SNPSIFT_COUNTOPNAME
3443
--snpsift_prevalOpName SNPSIFT_PREVALOPNAME
44+
--opOncoKbMafName OPONCOKBMAFNAME
45+
--oncoKbApiToken ONCOKBAPITOKEN
46+
--oncoKbAnnotateHotspots
47+
--input_complexity_bed INPUT_COMPLEXITY_BED
48+
--input_DUST_bed INPUT_DUST_BED
49+
--output_DUST_filename OUTPUT_DUST_FILENAME
50+
--column_name_DUST COLUMN_NAME_DUST
51+
--output_complexity_filename OUTPUT_COMPLEXITY_FILENAME
52+
--column_name_complexity COLUMN_NAME_COMPLEXITY
3553
```
3654

‎variant_annotation/example_inputs.yaml‎

Lines changed: 12 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,18 @@ input_cosmicprevalenceDB_vcf:
1111
/work/cch/production/resources/cosmic/versions/v96/CosmicCodingMuts_GRCh37_processed.vcf.gz
1212
snpsift_countOpName: tumorId_cosmic.vcf
1313
snpsift_prevalOpName: tumorId_preval.vcf
14-
output_mafName: tumorId_annotated.maf
14+
opOncoKbMafName: tumorId_annotated.maf
1515
retain_info: CNT,TUMOR_TYPE
1616
tumor_id: tumorId
1717
min_hom_vaf: 0
18+
column_name_mappability: mappability
19+
column_name_complexity: complexity
20+
input_mappability_bed:
21+
class: File
22+
path: /path/to/mappability_algo/bedfile.bed
23+
input_complexity_bed:
24+
class: File
25+
path: /path/to/complexity/bedfile.bed
26+
output_mappability_filename: mappability.maf
27+
output_complexity_filename: complexity.maf
28+
output_vcf2mafName: vcf2maf.maf

0 commit comments

Comments
 (0)