@platforma-open/milaboratories.immune-assay-data.workflow 1.9.0 → 1.10.0

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.
Files changed (13) hide show
  1. package/.turbo/turbo-build.log +1 -1
  2. package/CHANGELOG.md +6 -0
  3. package/dist/tengo/tpl/analysis.plj.gz +0 -0
  4. package/dist/tengo/tpl/build-outputs.plj.gz +0 -0
  5. package/dist/tengo/tpl/check-content-empty.plj.gz +0 -0
  6. package/dist/tengo/tpl/extract-unique-values.plj.gz +0 -0
  7. package/dist/tengo/tpl/get-unique-values.plj.gz +0 -0
  8. package/dist/tengo/tpl/main.plj.gz +0 -0
  9. package/dist/tengo/tpl/prerun.plj.gz +0 -0
  10. package/dist/tengo/tpl/process-outputs.plj.gz +0 -0
  11. package/dist/tengo/tpl/run-alignment.plj.gz +0 -0
  12. package/package.json +6 -6
  13. package/src/run-alignment.tpl.tengo +10 -3
package/.turbo/turbo-build.log CHANGED
@@ -1,6 +1,6 @@
1
1
   WARN  Issue while reading "/home/runner/work/immune-assay-data/immune-assay-data/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
2
2
 
3
- > @platforma-open/milaboratories.immune-assay-data.workflow@1.9.0 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
3
+ > @platforma-open/milaboratories.immune-assay-data.workflow@1.10.0 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
4
4
  > rm -rf dist && pl-tengo check && pl-tengo build
5
5
 
6
6
  Processing "src/analysis.tpl.tengo"...
package/CHANGELOG.md CHANGED
@@ -1,5 +1,11 @@
1
1
  # @platforma-open/milaboratories.immune-assay-data.workflow
2
2
 
3
+ ## 1.10.0
4
+
5
+ ### Minor Changes
6
+
7
+ - 29a44a2: Improved performance on large datasets
8
+
3
9
  ## 1.9.0
4
10
 
5
11
  ### Minor Changes
package/dist/tengo/tpl/analysis.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/build-outputs.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/main.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/prerun.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/run-alignment.plj.gz CHANGED
Binary file
package/package.json CHANGED
@@ -1,20 +1,20 @@
1
1
  {
2
2
  "name": "@platforma-open/milaboratories.immune-assay-data.workflow",
3
- "version": "1.9.0",
3
+ "version": "1.10.0",
4
4
  "type": "module",
5
5
  "description": "Tengo-based template",
6
6
  "dependencies": {
7
- "@platforma-sdk/workflow-tengo": "5.10.1",
7
+ "@platforma-sdk/workflow-tengo": "5.11.0",
8
8
  "@platforma-open/soedinglab.software-mmseqs2": "1.18.3",
9
9
  "@platforma-open/milaboratories.immune-assay-data.prepare-fasta": "1.1.3",
10
- "@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc": "1.2.0",
11
10
  "@platforma-open/milaboratories.immune-assay-data.add-header": "1.1.3",
11
+ "@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc": "1.2.0",
12
12
  "@platforma-open/milaboratories.immune-assay-data.fasta-to-tsv": "1.1.3",
13
- "@platforma-open/milaboratories.immune-assay-data.check-content-empty": "1.0.1",
14
- "@platforma-open/milaboratories.immune-assay-data.xlsx-to-csv": "1.1.0"
13
+ "@platforma-open/milaboratories.immune-assay-data.xlsx-to-csv": "1.1.0",
14
+ "@platforma-open/milaboratories.immune-assay-data.check-content-empty": "1.0.1"
15
15
  },
16
16
  "devDependencies": {
17
- "@platforma-sdk/tengo-builder": "2.4.30"
17
+ "@platforma-sdk/tengo-builder": "2.5.5"
18
18
  },
19
19
  "scripts": {
20
20
  "build": "rm -rf dist && pl-tengo check && pl-tengo build",
package/src/run-alignment.tpl.tengo CHANGED
@@ -2,6 +2,7 @@ self := import("@platforma-sdk/workflow-tengo:tpl")
2
2
  ll := import("@platforma-sdk/workflow-tengo:ll")
3
3
  exec := import("@platforma-sdk/workflow-tengo:exec")
4
4
  assets:= import("@platforma-sdk/workflow-tengo:assets")
5
+ math := import("math")
5
6
  mmseqsSw := assets.importSoftware("@platforma-open/soedinglab.software-mmseqs2:main")
6
7
 
7
8
  self.defineOutputs("mmseqsOutput")
@@ -16,15 +17,20 @@ self.body(func(args) {
16
17
  clonesFasta := args.clonesFasta
17
18
  assayFasta := args.assayFasta
18
19
 
19
- mem := "8GiB"
20
- cpu := 1
20
+ baseMemGiB := 64
21
21
  if !is_undefined(args.metaInputs.mem) {
22
- mem = string(args.metaInputs.mem) + "GiB"
22
+ baseMemGiB = args.metaInputs.mem
23
23
  }
24
+ mem := string(int(math.max(64, baseMemGiB))) + "GiB"
25
+ cpu := 1
24
26
  if !is_undefined(args.metaInputs.cpu) {
25
27
  cpu = args.metaInputs.cpu
26
28
  }
27
29
 
30
+ // Cap mmseqs2 in-RAM usage to 80% of allocated memory so it splits to disk
31
+ // rather than getting OOM-killed by the kernel on large datasets.
32
+ memLimit := "{int(ceil(system.ram.gb * 0.8))}" + "G"
33
+
28
34
  mmseqs := exec.builder().
29
35
  software(mmseqsSw).
30
36
  mem(mem).
@@ -34,6 +40,7 @@ self.body(func(args) {
34
40
  arg("clones.fasta").
35
41
  arg("results.tsv").
36
42
  arg("tmp").
43
+ arg("--split-memory-limit").argWithVar(memLimit).
37
44
  arg("--threads").arg(string(cpu)).
38
45
  arg("--max-seqs").arg("10000").
39
46
  arg("--search-type").arg(mmseqsSearchType).