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Sfitz update call sSNV to 8.0.0-rc.1 #153

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merged 35 commits into from
Dec 22, 2023
Merged

Sfitz update call sSNV to 8.0.0-rc.1 #153

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fc8a79f
Add option for running downstream pipelines serially
yashpatel6 Nov 30, 2023
c848659
Add validation for serialization parameter
yashpatel6 Nov 30, 2023
ddf4b09
Add validation for pipeline ordering parameter
yashpatel6 Nov 30, 2023
42e36fe
Add ordering resolution to methods
yashpatel6 Dec 1, 2023
c77063f
Add completion signal to call-gSNP
yashpatel6 Dec 1, 2023
e13606c
Add completion signal to call-gSV
yashpatel6 Dec 1, 2023
c298e96
Add completion signal to call-mtSNV
yashpatel6 Dec 1, 2023
ec244af
Add completion signal to call-sSNV
yashpatel6 Dec 1, 2023
630bdc5
Add completion signal to call-sSV
yashpatel6 Dec 1, 2023
dc86845
Add predecessor watcher for call-gSNP
yashpatel6 Dec 1, 2023
b7f2a5b
Add predecessor watcher for call-gSV
yashpatel6 Dec 1, 2023
ba73d73
Add predecessor watcher for call-mtSNV
yashpatel6 Dec 1, 2023
5c46e50
Add predecessor watcher for call-sSNV
yashpatel6 Dec 1, 2023
dbf2c1e
Add predecessor watcher for call-sSV
yashpatel6 Dec 1, 2023
9e38209
Make pipelines into list
yashpatel6 Dec 1, 2023
6cbec46
Remove print and use default_predecessor
yashpatel6 Dec 1, 2023
d008726
Add predecessors to params YAML
yashpatel6 Dec 1, 2023
60da57e
Ensure all enabled pipelines create status completion signals
yashpatel6 Dec 1, 2023
18c27c8
Fix infinite watcher in downstream pipelines
yashpatel6 Dec 2, 2023
c43a736
Merge branch 'main' into yashpatel-allow-pipeline-ordering
yashpatel6 Dec 7, 2023
cb1181c
Update tests with status check
yashpatel6 Dec 12, 2023
422f71e
Add status deletion function for testing
yashpatel6 Dec 13, 2023
b9ba8d2
Add status deletion to simulate pipeline completion
yashpatel6 Dec 13, 2023
e7ff352
Add predecessors to params in test-metapipeline-DNA
yashpatel6 Dec 13, 2023
7d41608
Update CHANGELOG
yashpatel6 Dec 13, 2023
30fa122
Add params to README
yashpatel6 Dec 13, 2023
a8fa618
changelog and sSNV input yaml
sorelfitzgibbon Dec 13, 2023
f9b12d6
update input yaml creation
sorelfitzgibbon Dec 13, 2023
92ddd5d
update nftest paths
sorelfitzgibbon Dec 13, 2023
01e1e40
update extracted sample names in nftest output file paths
sorelfitzgibbon Dec 13, 2023
5ebe49e
update extracted sample names in nftest output file paths
sorelfitzgibbon Dec 14, 2023
6600b51
nftest expected filepaths updated
sorelfitzgibbon Dec 19, 2023
d11147f
update call-sSNV
sorelfitzgibbon Dec 19, 2023
d8b114f
update nftest paths
sorelfitzgibbon Dec 19, 2023
1dab16f
merge in main
sorelfitzgibbon Dec 21, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
+ Pipeline ordering option for pipelines downstream of recalibrate-BAM
+ Parameter to run pipelines sequentially

### Changed
+ Call-sSNV: 7.0.0-rc.2 -> 8.0.0-rc.1

---

## [5.2.1] - 2023-12-07
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2 changes: 1 addition & 1 deletion external/pipeline-call-sSNV
Open in desktop
Submodule pipeline-call-sSNV updated 37 files
+4 −4 .github/PULL_REQUEST_TEMPLATE.md
+3 −2 .github/workflows/pipeline-release.yaml
+16 −0 CHANGELOG.md
+79 −32 README.md
+7 −7 config/base.config
+74 −2 config/custom_schema_types.config
+6 −3 config/default.config
+51 −99 config/methods.config
+14 −9 config/schema.yaml
+8 −4 config/template.config
+1 −1 external/pipeline-Nextflow-config
+1 −1 external/pipeline-Nextflow-module
+2 −4 input/call-sSNV-template-overwrite.yaml
+2 −4 input/call-sSNV-template.yaml
+3 −6 input/example-test-multi-sample.yaml
+1 −2 input/example-test-tumor-only.yaml
+2 −4 input/example-test.yaml
+62 −77 main.nf
+2 −2 metadata.yaml
+22 −18 module/common.nf
+9 −11 module/intersect.nf
+6 −4 module/muse.nf
+10 −35 module/mutect2-processes.nf
+52 −36 module/mutect2.nf
+9 −7 module/somaticsniper.nf
+17 −9 module/strelka2.nf
+1 −1 nextflow.config
+77 −93 nftest.yml
+7 −2 test/config/a_mini-all-tools.config
+4 −1 test/config/a_mini-muse.config
+5 −1 test/config/a_mini-mutect2.config
+5 −1 test/config/a_mini-somaticsniper.config
+5 −1 test/config/a_mini-strelka2.config
+1 −1 test/config/a_mini-two-tools.config
+4 −6 test/yaml/a_mini-multiple-samples.yaml
+2 −4 test/yaml/a_mini_n2-std-input.yaml
+1 −2 test/yaml/a_mini_n2-tumor-only.yaml
6 changes: 3 additions & 3 deletions module/call_sSNV/create_YAML_call_sSNV.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ import org.yaml.snakeyaml.Yaml
* Create input YAML file for the call-sSNV pipeline.
*
* Input:
* A tuple of two items:
* A tuple of four items:
* @param sample_id (String): Sample ID to be used for run
* @param normal_bam (String): Path to normal BAM
* @param tumor_bam (List): List of paths to tumor BAMs
Expand Down Expand Up @@ -32,8 +32,8 @@ process create_YAML_call_sSNV {

exec:
input_yaml = 'call_sSNV_input.yaml'
param_tumor_bams = tumor_bam.collect{ ['id': it[0], 'BAM': "${it[1]}" as String] }
param_normal_bam = normal_bam.collect{ ['id': it[0], 'BAM': "${it[1]}" as String] }
param_tumor_bams = tumor_bam.collect{ ['BAM': "${it[1]}" as String] }
param_normal_bam = normal_bam.collect{ ['BAM': "${it[1]}" as String] }
if (params.sample_mode == 'single') {
input_map = [
'patient_id': sample_id,
Expand Down
48 changes: 24 additions & 24 deletions nftest.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -68,41 +68,41 @@ cases:
verbose: true
skip: true
asserts:
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/BCFtools-1.17_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-concat.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/BCFtools-1.17_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-concat.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/BCFtools-1.17_LUAD0000034_CPT0053040010_SNV-concat.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/BCFtools-1.17_LUAD0000034_CPT0053040010_SNV-concat.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/MuSE-2.0.3_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/MuSE-2.0.2_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/MuSE-2.0.4_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/MuSE-2.0.4_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/SomaticSniper-1.0.5.0_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV-intersect.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Strelka2-2.9.10_LUAD0000034_CPT0053040010_SNV-intersect.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/MuSE-2.0.3/output/MuSE-2.0.3_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/MuSE-2.0.2_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/MuSE-2.0.4/output/MuSE-2.0.4_LUAD0000034_CPT0053040010_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/MuSE-2.0.4_LUAD0000034_CPT0053040010_SNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/SomaticSniper-1.0.5.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_LUAD0000034_CPT0053040010_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/SomaticSniper-1.0.5.0_LUAD0000034_CPT0053040010_SNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_CPT0053040010_Indel.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Strelka2-2.9.10_LUAD0000034_CPT0053040010_Indel.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Strelka2-2.9.10_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Strelka2-2.9.10/output/Strelka2-2.9.10_LUAD0000034_CPT0053040010_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Strelka2-2.9.10_LUAD0000034_CPT0053040010_SNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_Indel.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_Indel.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_Indel.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_MNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_MNV.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_MNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_MNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-7.0.0-rc.2/GZLUCPTA000001-T001-P01-F/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/GZLUCPTA000001-T001-P01-F/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_GZLUCPTA000001-T001-P01-F_SNV.vcf.gz
- actual: output/call-sSNV-*/CPT0053040010/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/germline-somatic/1.0.0/test-output/test-call-sSNV/GZLUCPTA000001/CPT0053040010/call_sSNV/Mutect2-4.4.0.0_LUAD0000034_CPT0053040010_SNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh


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