@platforma-open/milaboratories.mixcr-amplicon-alignment.workflow 1.21.10 → 1.21.11
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/CHANGELOG.md +6 -0
- package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
- package/dist/tengo/tpl/export-report.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.plj.gz +0 -0
- package/dist/tengo/tpl/repseqio-library.plj.gz +0 -0
- package/package.json +1 -1
- package/src/main.tpl.tengo +1 -0
- package/src/mixcr-analyze.tpl.tengo +6 -0
- package/src/process.tpl.tengo +1 -0
package/.turbo/turbo-build.log
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
WARN Issue while reading "/home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
|
|
2
2
|
|
|
3
|
-
> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.21.
|
|
3
|
+
> @platforma-open/milaboratories.mixcr-amplicon-alignment.workflow@1.21.11 build /home/runner/work/mixcr-amplicon-alignment/mixcr-amplicon-alignment/workflow
|
|
4
4
|
> rm -rf dist && pl-tengo check && pl-tengo build
|
|
5
5
|
|
|
6
6
|
Processing "src/aggregate-by-clonotype-key.tpl.tengo"...
|
package/CHANGELOG.md
CHANGED
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
|
Binary file
|
package/package.json
CHANGED
package/src/main.tpl.tengo
CHANGED
|
@@ -144,6 +144,7 @@ wf.body(func(args) {
|
|
|
144
144
|
assemblingFeature: args.assemblingFeature,
|
|
145
145
|
imputeGermline: args.imputeGermline,
|
|
146
146
|
badQualityThreshold: args.badQualityThreshold,
|
|
147
|
+
disableLowQualityMapping: args.disableLowQualityMapping,
|
|
147
148
|
isLibraryFileGzipped: isLibraryFileGzipped,
|
|
148
149
|
stopCodonTypes: args.stopCodonTypes,
|
|
149
150
|
stopCodonReplacements: args.stopCodonReplacements
|
|
@@ -122,6 +122,12 @@ self.body(func(inputs) {
|
|
|
122
122
|
mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.minimalQuality=" + string(int(badQualityThreshold)))
|
|
123
123
|
}
|
|
124
124
|
|
|
125
|
+
// Disable the deferred-reads mapping phase
|
|
126
|
+
disableLowQualityMapping := params.disableLowQualityMapping
|
|
127
|
+
if !is_undefined(disableLowQualityMapping) && disableLowQualityMapping {
|
|
128
|
+
mixcrCmdBuilder.arg("-Massemble.cloneAssemblerParameters.maxBadPointsPercent=0")
|
|
129
|
+
}
|
|
130
|
+
|
|
125
131
|
// if (!is_undefined(threePrimePrimer)) {
|
|
126
132
|
// mixcrCmdBuilder.arg("--floating-left-alignment-boundary")
|
|
127
133
|
// } else {
|
package/src/process.tpl.tengo
CHANGED
|
@@ -221,6 +221,7 @@ self.body(func(inputs) {
|
|
|
221
221
|
assemblingFeature: params.assemblingFeature,
|
|
222
222
|
imputeGermline: params.imputeGermline,
|
|
223
223
|
badQualityThreshold: params.badQualityThreshold,
|
|
224
|
+
disableLowQualityMapping: params.disableLowQualityMapping,
|
|
224
225
|
isLibraryFileGzipped: params.isLibraryFileGzipped
|
|
225
226
|
}, { removeUndefs: true }),
|
|
226
227
|
limitInput: limitInput
|