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nftest.yaml
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---
global:
temp_dir: ./test/work
nf_config: test/global.config
remove_temp: false
clean_logs: true
cases:
- name: test-bam2fastq
message: Test convert-BAM2FASTQ
nf_script: test/test-bam2fastq/test.nf
nf_config: test/test-bam2fastq/test.config
verbose: true
skip: true
asserts:
- actual: output/convert-BAM2FASTQ-*/NA24149/SAMtools-*/output/SAMtools-1.19.2_IlluminaTest_NA24149_NA24149RG.Seq1-0-R1.fastq.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/convert-BAM2FASTQ-2.0.0-rc.2/NA24149/SAMtools-1.15.1/output/NA24149RG.Seq1_collated_R1.fq.gz
script: test/test-bam2fastq/assert_fastq.sh
- actual: output/convert-BAM2FASTQ-*/NA24149/SAMtools-*/output/SAMtools-1.19.2_IlluminaTest_NA24149_NA24149RG.Seq1-0-R2.fastq.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/convert-BAM2FASTQ-2.0.0-rc.2/NA24149/SAMtools-1.15.1/output/NA24149RG.Seq1_collated_R2.fq.gz
script: test/test-bam2fastq/assert_fastq.sh
- name: test-align-DNA
message: Test align-DNA
nf_script: test/test-align-DNA/test.nf
nf_config: test/test-align-DNA/test.config
verbose: true
skip: true
# Disabling BAM comparisons since there can be variability based on number of threads used
- name: test-recalibrate-BAM
message: Test recalibrate-BAM
nf_script: test/test-recalibrate-BAM/test.nf
nf_config: test/test-recalibrate-BAM/test.config
verbose: true
skip: true
- name: test-calculate-targeted-coverage
message: Test calculate-targeted-coverage
nf_script: test/test-calculate-targeted-coverage/test.nf
nf_config: test/test-calculate-targeted-coverage/test.config
verbose: true
skip: true
asserts:
- actual: output/calculate-targeted-coverage-*/NA24149/SAMtools-*/output/BEDtools-*collapsed-coverage.bed
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/calculate-targeted-coverage-1.0.0-rc.2/NA24149/SAMtools-1.16.1/output/NA24149.collapsed_coverage.bed
script: test/test-calculate-targeted-coverage/assert_bed.sh
- actual: output/calculate-targeted-coverage-*/NA24149/SAMtools-*/output/BEDtools-*off-target-dbSNP-depth-per-base.bed
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/calculate-targeted-coverage-1.0.0-rc.2/NA24149/SAMtools-1.16.1/output/NA24149.off-target-dbSNP_depth-per-base.bed
script: test/test-calculate-targeted-coverage/assert_bed.sh
- actual: output/calculate-targeted-coverage-*/NA24149/SAMtools-*/output/BEDtools-*target-with-enriched-off-target-intervals.bed.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/calculate-targeted-coverage-1.0.0-rc.2/NA24149/SAMtools-1.16.1/output/BEDtools-2.29.2_IlluminaTest_NA24149_target-with-enriched-off-target-intervals.bed.gz
script: test/test-calculate-targeted-coverage/assert_bed.sh
- name: test-generate-SQC-BAM
message: Test generate-SQC-BAM pipeline
nf_script: test/test-generate-SQC-BAM/test.nf
nf_config: test/test-generate-SQC-BAM/test.config
verbose: true
skip: true
asserts:
- actual: output/generate-SQC-BAM-*/IlluminaPatient1/SAMtools-*/output/SAMtools-*_IlluminaTest_NA24143_stats.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/generate-SQC-BAM-1.0.0/IlluminaPatient1/SAMtools-1.18/output/SAMtools-1.18_IlluminaTest_NA24143_stats.txt
method: md5
- actual: output/generate-SQC-BAM-*/IlluminaPatient1/SAMtools-*/output/SAMtools-*_IlluminaTest_NA24149_stats.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/generate-SQC-BAM-1.0.0/IlluminaPatient1/SAMtools-1.18/output/SAMtools-1.18_IlluminaTest_NA24149_stats.txt
method: md5
- actual: output/generate-SQC-BAM-*/IlluminaPatient1/Picard-*/output/Picard-*_IlluminaTest_NA24143_wgs-metrics.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/generate-SQC-BAM-1.0.0/IlluminaPatient1/Picard-3.1.0/output/Picard-3.1.0_IlluminaTest_NA24143_wgs-metrics.txt
script: test/test-generate-SQC-BAM/assert_metrics.sh
- actual: output/generate-SQC-BAM-*/IlluminaPatient1/Picard-*/output/Picard-*_IlluminaTest_NA24149_wgs-metrics.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/generate-SQC-BAM-1.0.0/IlluminaPatient1/Picard-3.1.0/output/Picard-3.1.0_IlluminaTest_NA24149_wgs-metrics.txt
script: test/test-generate-SQC-BAM/assert_metrics.sh
- name: test-call-gSNP
message: Test call-gSNP with one tumor normal pair
nf_script: test/test-call-gSNP/test.nf
nf_config: test/test-call-gSNP/test.config
verbose: true
skip: true
asserts:
- actual: output/call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24143.g.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSNP-10.0.0-rc.3/NA24143/GATK-4.2.4.1/output/GATK-*_IlluminaTest_NA24143.g.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-gSNP-*/NA24143/GATK-*/output/GATK-*_IlluminaTest_NA24149.g.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSNP-10.0.0-rc.3/NA24143/GATK-4.2.4.1/output/GATK-*_IlluminaTest_NA24149.g.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
# Pending enablement until direct entry-point is added
# - name: test-StableLiftsSNV
# message: Test StableLift with sSNV input
# nf_script: test/test-StableLiftsSNV/test.nf
# nf_config: test/test-StableLiftsSNV/test.config
# verbose: true
# skip: true
# asserts:
# - actual:
# expect:
# script: test/test-call-gSNP/assert_vcf.sh
- name: test-call-sSNV
message: Test call-sSNV with one tumor normal pair
nf_script: test/test-call-sSNV/test.nf
nf_config: test/test-call-sSNV/test.config
verbose: true
skip: true
asserts:
- actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/BCFtools-*_IlluminaTest_NA24143_SNV-concat.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/BCFtools-1.17_IlluminaTest_NA24143_SNV-concat.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/MuSE-*_IlluminaTest_NA24143_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/MuSE-2.0.4_IlluminaTest_NA24143_SNV-intersect.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/Mutect2-*_IlluminaTest_NA24143_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/Mutect2-4.4.0.0_IlluminaTest_NA24143_SNV-intersect.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/SomaticSniper-*_IlluminaTest_NA24143_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/SomaticSniper-1.0.5.0_IlluminaTest_NA24143_SNV-intersect.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Intersect-BCFtools-*/output/Strelka2-*_IlluminaTest_NA24143_SNV-intersect.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Intersect-BCFtools-1.17/output/Strelka2-2.9.10_IlluminaTest_NA24143_SNV-intersect.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/MuSE-*/output/MuSE-*_IlluminaTest_NA24143_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/MuSE-2.0.4/output/MuSE-2.0.4_IlluminaTest_NA24143_SNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/SomaticSniper-*/output/SomaticSniper-*_IlluminaTest_NA24143_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/SomaticSniper-1.0.5.0/output/SomaticSniper-1.0.5.0_IlluminaTest_NA24143_SNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Strelka2-*/output/Strelka2-*_IlluminaTest_NA24143_Indel.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Strelka2-2.9.10/output/Strelka2-2.9.10_IlluminaTest_NA24143_Indel.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Strelka2-*/output/Strelka2-*_IlluminaTest_NA24143_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Strelka2-2.9.10/output/Strelka2-2.9.10_IlluminaTest_NA24143_SNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Mutect2-*/output/Mutect2-*_IlluminaTest_NA24143_Indel.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_IlluminaTest_NA24143_Indel.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Mutect2-*/output/Mutect2-*_IlluminaTest_NA24143_MNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_IlluminaTest_NA24143_MNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSNV-*/NA24143/Mutect2-*/output/Mutect2-*_IlluminaTest_NA24143_SNV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSNV-8.0.0-rc.1/NA24143/Mutect2-4.4.0.0/output/Mutect2-4.4.0.0_IlluminaTest_NA24143_SNV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- name: test-call-mtSNV
message: Test call-mtSNV pipeline with one tumor normal pair
nf_script: test/test-call-mtSNV/test.nf
nf_config: test/test-call-mtSNV/test.config
verbose: true
skip: true
asserts:
- actual: output/call-mtSNV-*/NA24143/mitoCaller-*/output/mitoCaller2vcf-*_IlluminaTest_NA24143.vcf
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-mtSNV-3.0.0/NA24143/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_IlluminaTest_NA24143.vcf
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-mtSNV-*/NA24143/mitoCaller-*/output/mitoCaller2vcf-*_IlluminaTest_NA24143_homoplasmy.vcf
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-mtSNV-3.0.0/NA24143/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_IlluminaTest_NA24143_homoplasmy.vcf
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-mtSNV-*/NA24143/mitoCaller-*/output/mitoCaller2vcf-*_IlluminaTest_NA24149.vcf
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-mtSNV-3.0.0/NA24143/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_IlluminaTest_NA24149.vcf
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-mtSNV-*/NA24143/mitoCaller-*/output/mitoCaller2vcf-*_IlluminaTest_NA24149_homoplasmy.vcf
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-mtSNV-3.0.0/NA24143/mitoCaller-1.0.0/output/mitoCaller2vcf-1.0.0_IlluminaTest_NA24149_homoplasmy.vcf
script: test/test-call-gSNP/assert_vcf.sh
- name: test-call-gSV
message: Test call-gSV pipeline with one tumor normal pair
nf_script: test/test-call-gSV/test.nf
nf_config: test/test-call-gSV/test.config
verbose: true
skip: true
asserts:
- actual: output/call-gSV-*/NA24149/Manta-*/output/Manta-*_IlluminaTest_NA24149_diploidSV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSV-4.0.1/NA24149/Manta-1.6.0/output/diploidSV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-gSV-*/NA24149/Manta-*/output/Manta-*_IlluminaTest_NA24149_candidateSV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSV-4.0.1/NA24149/Manta-1.6.0/output/candidateSV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-gSV-*/NA24149/Manta-*/output/Manta-*_IlluminaTest_NA24149_candidateSmallIndels.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-gSV-4.0.1/NA24149/Manta-1.6.0/output/candidateSmallIndels.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- name: test-call-sSV
message: Test call-sSV pipeline with one tumor normal pair
nf_script: test/test-call-sSV/test.nf
nf_config: test/test-call-sSV/test.config
verbose: true
skip: true
asserts:
- actual: output/call-sSV-*/NA24143/DELLY-*/output/DELLY-*_IlluminaTest_NA24143.bcf
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.1.0/NA24143/DELLY-1.2.6/output/DELLY-1.2.6_IlluminaTest_NA24143.bcf
script: test/test-call-gSV/assert_bcf.sh
- actual: output/call-sSV-*/NA24143/Manta-*/output/Manta-*_IlluminaTest_NA24143_diploidSV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.1.0/NA24143/Manta-1.6.0/output/Manta-1.6.0_IlluminaTest_NA24143_diploidSV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSV-*/NA24143/Manta-*/output/Manta-*_IlluminaTest_NA24143_candidateSV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.1.0/NA24143/Manta-1.6.0/output/Manta-1.6.0_IlluminaTest_NA24143_candidateSV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSV-*/NA24143/Manta-*/output/Manta-*_IlluminaTest_NA24143_candidateSmallIndels.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.1.0/NA24143/Manta-1.6.0/output/Manta-1.6.0_IlluminaTest_NA24143_candidateSmallIndels.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- actual: output/call-sSV-*/NA24143/Manta-*/output/Manta-*_IlluminaTest_NA24143_somaticSV.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sSV-6.1.0/NA24143/Manta-1.6.0/output/Manta-1.6.0_IlluminaTest_NA24143_somaticSV.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- name: test-call-sCNA-cnv-facets
message: Test call-sCNA pipeline with one tumor normal pair and cnv_facets as the CNA caller
nf_script: test/test-call-sCNA/test.nf
nf_config: test/test-call-sCNA/test-cnv_facets.config
verbose: true
skip: true
asserts:
- actual: output/call-sCNA-*/NA24143/cnv_facets-*/output/CNV-FACETS-*_IlluminaTest_NA24143.vcf.gz
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/call-sCNA-cnv-facets-3.0.0/NA24143/cnv_facets-0.16.0/output/CNV-FACETS-0.16.0_IlluminaTest_NA24143.vcf.gz
script: test/test-call-gSNP/assert_vcf.sh
- name: test-call-sCNA-Battenberg
message: Test call-sCNA pipeline with one tumor normal pair and Battenberg as the CNA caller
nf_script: test/test-call-sCNA/test.nf
nf_config: test/test-call-sCNA/test-Battenberg.config
verbose: true
skip: true
- name: test-metapipeline-DNA
message: Test calling all pipelines with one tumor normal pair
nf_script: module/metapipeline_DNA.nf
nf_config: test/test-metapipeline-DNA/test.config
params_file: test/test-metapipeline-DNA/pipeline_specific_params.json
verbose: true
skip: true
- name: test-metapipeline-DNA-batch
message: Test running the main.nf that runs the metapipeline-DNA pipeline in batch.
nf_script: main.nf
nf_config: test/test-metapipeline-DNA-batch/test.config
verbose: true
skip: true
- name: test-metapipeline-DNA-fastq-input
message: Test running the main.nf that runs the metapipeline-DNA pipeline in batch with fastq inputs.
nf_script: main.nf
nf_config: test/test-metapipeline-DNA-fastq-input/test.config
params_file: test/test-metapipeline-DNA-fastq-input/input.yaml
verbose: true
skip: true
- name: test-config-pass
message: Test passing configuration
nf_script: main.nf
nf_config: test/test-config/pass.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/pass.txt
method: md5
- name: test-sSV-bad-algorithm
message: Test bad algorithm given for call-sSV
nf_script: main.nf
nf_config: test/test-config/ssv-bad-algorithm.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/ssv-bad-algorithm.txt
method: md5
- name: test-sCNA-bad-reference
message: Test bad reference given for call-sSV
nf_script: main.nf
nf_config: test/test-config/scna-bad-reference.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/scna-bad-reference.txt
method: md5
- name: test-mismatch-CNA-selection
message: Test mismatching selection of CNA algorithms for call-sCNA and call-SRC
nf_script: main.nf
nf_config: test/test-config/mismatch-cna-selection.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/mismatch-cna-selection.txt
method: md5
- name: test-mismatch-SNV-selection
message: Test mismatching selection of SNV algorithms for call-sSNV and call-SRC
nf_script: main.nf
nf_config: test/test-config/mismatch-snv-selection.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/mismatch-snv-selection.txt
method: md5
- name: test-missing-common-CSV-columns
message: Test missing common input CSV columns
nf_script: main.nf
nf_config: test/test-config/missing-common-csv.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/missing-common-csv-columns.txt
method: md5
- name: test-one-state-one-sample
message: Test each sample only given one state
nf_script: main.nf
nf_config: test/test-config/multiple-state.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/multiple-state.txt
method: md5
- name: test-multiple-BAMs-per-sample
message: Test each sample only given one BAM
nf_script: main.nf
nf_config: test/test-config/multiple-bams.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/multiple-bams.txt
method: md5
- name: test-no-pipelines-run
message: Test proper handling when no pipelines are resolved to run
nf_script: main.nf
nf_config: test/test-config/no-pipelines.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/no-pipelines.txt
method: md5
- name: test-duplicate-samples
message: Test detection of duplicate samples
nf_script: main.nf
nf_config: test/test-config/duplicate-sample.config
verbose: true
skip: true
asserts:
- actual: errors.txt
expect: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/output/test-config/duplicate-sample.txt
method: md5