@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.14.0 → 2.14.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.turbo/turbo-build.log +1 -1
- package/.turbo/turbo-test.log +10 -10
- package/CHANGELOG.md +12 -0
- package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
- package/dist/tengo/tpl/calculate-preset-info.plj.gz +0 -0
- package/dist/tengo/tpl/list-presets.plj.gz +0 -0
- package/dist/tengo/tpl/main.plj.gz +0 -0
- package/dist/tengo/tpl/mixcr-analyze.plj.gz +0 -0
- package/dist/tengo/tpl/mixcr-export.plj.gz +0 -0
- package/dist/tengo/tpl/prerun.plj.gz +0 -0
- package/dist/tengo/tpl/process-single-cell.plj.gz +0 -0
- package/dist/tengo/tpl/process.plj.gz +0 -0
- package/dist/tengo/tpl/test.columns-calculate.plj.gz +0 -0
- package/dist/tengo/tpl/test.columns.test.plj.gz +0 -0
- package/package.json +4 -4
- package/src/mixcr-export.tpl.tengo +3 -1
package/.turbo/turbo-build.log
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
WARN Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
|
|
2
2
|
|
|
3
|
-
> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.14.
|
|
3
|
+
> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.14.2 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
|
|
4
4
|
> rm -rf dist && pl-tengo check && pl-tengo build
|
|
5
5
|
|
|
6
6
|
info: Skipping unknown file type: test/columns.test.ts
|
package/.turbo/turbo-test.log
CHANGED
|
@@ -1,21 +1,21 @@
|
|
|
1
1
|
WARN Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
|
|
2
2
|
|
|
3
|
-
> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.14.
|
|
3
|
+
> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.14.2 test /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
|
|
4
4
|
> vitest
|
|
5
5
|
|
|
6
6
|
|
|
7
7
|
[1m[7m[36m RUN [39m[27m[22m [36mv2.1.8 [39m[90m/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow[39m
|
|
8
8
|
|
|
9
|
-
[32m✓[39m src/test/columns.test.ts [2m([22m[2m6 tests[22m[2m)[22m[33m
|
|
10
|
-
[33m[2m✓[22m[39m checking preset for 'milab-human-dna-xcr-7genes-multiplex' [
|
|
11
|
-
[33m[2m✓[22m[39m checking preset for '10x-sc-xcr-vdj' [
|
|
12
|
-
[33m[2m✓[22m[39m checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' [
|
|
13
|
-
[33m[2m✓[22m[39m checking preset for 'takara-human-rna-bcr-umi-smartseq' [
|
|
14
|
-
[33m[2m✓[22m[39m checking preset for 'rna-seq' [
|
|
15
|
-
[33m[2m✓[22m[39m checking preset for 'generic-single-cell-gex' [
|
|
9
|
+
[32m✓[39m src/test/columns.test.ts [2m([22m[2m6 tests[22m[2m)[22m[33m 53783[2mms[22m[39m
|
|
10
|
+
[33m[2m✓[22m[39m checking preset for 'milab-human-dna-xcr-7genes-multiplex' [33m13009[2mms[22m[39m
|
|
11
|
+
[33m[2m✓[22m[39m checking preset for '10x-sc-xcr-vdj' [33m8376[2mms[22m[39m
|
|
12
|
+
[33m[2m✓[22m[39m checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' [33m8245[2mms[22m[39m
|
|
13
|
+
[33m[2m✓[22m[39m checking preset for 'takara-human-rna-bcr-umi-smartseq' [33m8167[2mms[22m[39m
|
|
14
|
+
[33m[2m✓[22m[39m checking preset for 'rna-seq' [33m7998[2mms[22m[39m
|
|
15
|
+
[33m[2m✓[22m[39m checking preset for 'generic-single-cell-gex' [33m7987[2mms[22m[39m
|
|
16
16
|
|
|
17
17
|
[2m Test Files [22m [1m[32m1 passed[39m[22m[90m (1)[39m
|
|
18
18
|
[2m Tests [22m [1m[32m6 passed[39m[22m[90m (6)[39m
|
|
19
|
-
[2m Start at [22m
|
|
20
|
-
[2m Duration [22m
|
|
19
|
+
[2m Start at [22m 08:20:54
|
|
20
|
+
[2m Duration [22m 54.58s[2m (transform 43ms, setup 0ms, collect 565ms, tests 53.78s, environment 0ms, prepare 59ms)[22m
|
|
21
21
|
|
package/CHANGELOG.md
CHANGED
|
@@ -1,5 +1,17 @@
|
|
|
1
1
|
# @platforma-open/milaboratories.mixcr-clonotyping.workflow
|
|
2
2
|
|
|
3
|
+
## 2.14.2
|
|
4
|
+
|
|
5
|
+
### Patch Changes
|
|
6
|
+
|
|
7
|
+
- 7a78090: Drop logs in mixcr export to prevent CID conflicts in results deduplication
|
|
8
|
+
|
|
9
|
+
## 2.14.1
|
|
10
|
+
|
|
11
|
+
### Patch Changes
|
|
12
|
+
|
|
13
|
+
- 748457a: Upgrade mixcr version to prevent crash with custom library with custom C gene names
|
|
14
|
+
|
|
3
15
|
## 2.14.0
|
|
4
16
|
|
|
5
17
|
### Minor Changes
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
package/package.json
CHANGED
|
@@ -1,15 +1,15 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
|
|
3
|
-
"version": "2.14.
|
|
3
|
+
"version": "2.14.2",
|
|
4
4
|
"description": "Tengo-based template",
|
|
5
5
|
"dependencies": {
|
|
6
6
|
"@platforma-sdk/workflow-tengo": "^4.1.2",
|
|
7
|
-
"@platforma-open/milaboratories.mixcr-clonotyping-2.
|
|
8
|
-
"@platforma-open/milaboratories.mixcr-clonotyping-2.
|
|
7
|
+
"@platforma-open/milaboratories.mixcr-clonotyping-2.hash-column": "1.1.1",
|
|
8
|
+
"@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.3"
|
|
9
9
|
},
|
|
10
10
|
"devDependencies": {
|
|
11
11
|
"@platforma-sdk/tengo-builder": "^2.1.0",
|
|
12
|
-
"@platforma-open/milaboratories.software-mixcr": "4.7.0-
|
|
12
|
+
"@platforma-open/milaboratories.software-mixcr": "4.7.0-165-develop",
|
|
13
13
|
"@platforma-open/milaboratories.software-ptransform": "^1.3.1",
|
|
14
14
|
"@platforma-sdk/test": "^1.29.17",
|
|
15
15
|
"vitest": "~2.1.8",
|
|
@@ -32,6 +32,7 @@ self.body(func(inputs) {
|
|
|
32
32
|
mixcrCmdBuilder := exec.builder().
|
|
33
33
|
inMediumQueue().
|
|
34
34
|
printErrStreamToStdout().
|
|
35
|
+
dontSaveStdoutOrStderr().
|
|
35
36
|
software(mixcrSw).
|
|
36
37
|
secret("MI_LICENSE", "MI_LICENSE").
|
|
37
38
|
arg("exportClones").
|
|
@@ -56,6 +57,7 @@ self.body(func(inputs) {
|
|
|
56
57
|
addFile("clones.clns", clnsFile).
|
|
57
58
|
arg("clones.tsv").
|
|
58
59
|
saveFile("clones.tsv").
|
|
60
|
+
cacheHours(3).
|
|
59
61
|
run()
|
|
60
62
|
}
|
|
61
63
|
|
|
@@ -75,7 +77,7 @@ self.body(func(inputs) {
|
|
|
75
77
|
|
|
76
78
|
if is_undefined(clonotypeKeyColumns) {
|
|
77
79
|
result.tsv = unprocessedTsv
|
|
78
|
-
|
|
80
|
+
|
|
79
81
|
} else if is_undefined(cellTagColumns) {
|
|
80
82
|
hashCmdBuilder := exec.builder().
|
|
81
83
|
printErrStreamToStdout().
|