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nftest.yml
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nftest.yml
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---
global:
temp_dir: test/work
nf_config: test/global.config
remove_temp: true
clean_logs: true
cases:
- name: hg003-all-tools
message: test all tools with downsampled HG003 subsetted to 6 readgroups and 3 libraries; sample level fastqc
nf_script: main.nf
nf_config: test/config/all-tools.config
params_file: test/yaml/HG003_0.05x-selected-readgroups.yaml
skip: false
verbose: true
asserts:
- actual: generate-SQC-BAM-*/NA24149/FastQC-*/output/by-sample/FastQC-*_GIAB_HG003_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_GIAB_HG003_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-sample/SAMtools-*_GIAB_HG003_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-library/SAMtools-*_GIAB_HG003-HG003.H9YY4ADXX.3F1_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.H9YY4ADXX.3F1_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-library/SAMtools-*_GIAB_HG003-HG003.HA0L6ADXX.3F1_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.HA0L6ADXX.3F1_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-library/SAMtools-*_GIAB_HG003-HG003.HA660ADXX.3L1_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.HA660ADXX.3L1_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-readgroup/SAMtools-*_GIAB_HG003-HG003.H9YY4ADXX.3F1-HG003.H9YY4ADXX.3F1.L002-001.SeqL002-001_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.H9YY4ADXX.3F1-HG003.H9YY4ADXX.3F1.L002-001.SeqL002-001_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-readgroup/SAMtools-*_GIAB_HG003-HG003.HA0L6ADXX.3F1-HG003.HA0L6ADXX.3F1.L001-001.SeqL001-001_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.HA0L6ADXX.3F1-HG003.HA0L6ADXX.3F1.L001-001.SeqL001-001_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-readgroup/SAMtools-*_GIAB_HG003-HG003.HA0L6ADXX.3F1-HG003.HA0L6ADXX.3F1.L002-001.SeqL002-001_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.HA0L6ADXX.3F1-HG003.HA0L6ADXX.3F1.L002-001.SeqL002-001_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-readgroup/SAMtools-*_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L001-001.SeqL001-001_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L001-001.SeqL001-001_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-readgroup/SAMtools-*_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L002-002.SeqL002-002_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L002-002.SeqL002-002_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/SAMtools-*/output/by-readgroup/SAMtools-*_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L002-005.SeqL002-005_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L002-005.SeqL002-005_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/Picard-3.1.0/output/Picard-3.1.0_GIAB_HG003_wgs-metrics.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_GIAB_HG003_wgs-metrics.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/Qualimap-2.3/output/Qualimap-2.3_GIAB_HG003_stats/genome_results.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_GIAB_HG003_stats/genome_results.txt
script: test/assert_txt.sh
- name: a_mini-all-tools
message: test all tools with a_mini, single readgroup normal and tumor
nf_script: main.nf
nf_config: test/config/all-tools.config
params_file: test/yaml/a_mini.yaml
skip: false
verbose: true
asserts:
- actual: generate-SQC-BAM-*/TWGSAMIN000001/FastQC-*/output/by-sample/FastQC-*_TWGSAMIN_HG002.N_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_TWGSAMIN_HG002.N_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/FastQC-*/output/by-sample/FastQC-*_TWGSAMIN_S2-v1.1.5_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_TWGSAMIN_S2-v1.1.5_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/by-sample/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_TWGSAMIN_HG002.N_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/by-sample/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_TWGSAMIN_S2-v1.1.5_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
method: md5
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
method: md5
- name: a_mini-multiple-samples-all-tools
message: test all tools with 1 normal and 2 tumor samples (single readgroups)
nf_script: main.nf
nf_config: test/config/all-tools.config
params_file: test/yaml/a_mini-multiple-samples.yaml
skip: false
verbose: true
asserts:
- actual: generate-SQC-BAM-*/TWGSAMIN000001/FastQC-*/output/by-sample/FastQC-*_TWGSAMIN_HG002.N_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_TWGSAMIN_HG002.N_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/FastQC-*/output/by-sample/FastQC-*_TWGSAMIN_S2-v1.1.5_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_TWGSAMIN_S2-v1.1.5_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/FastQC-*/output/by-sample/FastQC-*_TWGSAMIN_S2-v1.1.5.n1_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_TWGSAMIN_S2-v1.1.5.n1_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/by-sample/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_TWGSAMIN_HG002.N_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/by-sample/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_TWGSAMIN_S2-v1.1.5_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/by-sample/SAMtools-*_TWGSAMIN_S2-v1.1.5.n1_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_TWGSAMIN_S2-v1.1.5.n1_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5.n1_wgs-metrics.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5.n1_wgs-metrics.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
method: md5
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
method: md5
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5.n1_stats/genome_results.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5.n1_stats/genome_results.txt
method: md5
- name: hg003-fastqc
message: test fastqc with downsampled HG003 subsetted to 6 readgroups and 3 libraries, readgroup level
nf_script: main.nf
nf_config: test/config/fastqc-readgroup.config
params_file: test/yaml/HG003_0.05x-selected-readgroups.yaml
skip: true
verbose: true
asserts:
- actual: generate-SQC-BAM-*/NA24149/FastQC-*/output/by-readgroup/FastQC-*_GIAB_HG003-HG003.H9YY4ADXX.3F1-HG003.H9YY4ADXX.3F1.L002-001.SeqL002-001_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_GIAB_HG003-HG003.H9YY4ADXX.3F1-HG003.H9YY4ADXX.3F1.L002-001.SeqL002-001_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/FastQC-*/output/by-readgroup/FastQC-*_GIAB_HG003-HG003.HA0L6ADXX.3F1-HG003.HA0L6ADXX.3F1.L001-001.SeqL001-001_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_GIAB_HG003-HG003.HA0L6ADXX.3F1-HG003.HA0L6ADXX.3F1.L001-001.SeqL001-001_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/FastQC-*/output/by-readgroup/FastQC-*_GIAB_HG003-HG003.HA0L6ADXX.3F1-HG003.HA0L6ADXX.3F1.L002-001.SeqL002-001_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_GIAB_HG003-HG003.HA0L6ADXX.3F1-HG003.HA0L6ADXX.3F1.L002-001.SeqL002-001_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/FastQC-*/output/by-readgroup/FastQC-*_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L001-001.SeqL001-001_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L001-001.SeqL001-001_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/FastQC-*/output/by-readgroup/FastQC-*_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L002-002.SeqL002-002_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L002-002.SeqL002-002_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/NA24149/FastQC-*/output/by-readgroup/FastQC-*_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L002-005.SeqL002-005_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_GIAB_HG003-HG003.HA660ADXX.3L1-HG003.HA660ADXX.3L1.L002-005.SeqL002-005_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- name: a_mini-fastqc
message: test fastqc with a_mini normal and tumor, sample level
nf_script: main.nf
nf_config: test/config/fastqc-sample.config
params_file: test/yaml/a_mini.yaml
skip: true
verbose: true
asserts:
- actual: generate-SQC-BAM-*/TWGSAMIN000001/FastQC-*/output/by-sample/FastQC-*_TWGSAMIN_HG002.N_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_TWGSAMIN_HG002.N_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/FastQC-*/output/by-sample/FastQC-*_TWGSAMIN_S2-v1.1.5_fastqc/fastqc_data.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/FastQC-0.12.1-samtools-1.20_TWGSAMIN_S2-v1.1.5_fastqc/fastqc_data.txt
script: test/assert_txt.sh
- name: a_mini-stats
message: test samtools stats
nf_script: main.nf
nf_config: test/config/stats.config
params_file: test/yaml/a_mini.yaml
skip: true
verbose: true
asserts:
- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/by-sample/SAMtools-*_TWGSAMIN_HG002.N_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_TWGSAMIN_HG002.N_stats.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/SAMtools-*/output/by-sample/SAMtools-*_TWGSAMIN_S2-v1.1.5_stats.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/SAMtools-1.20_TWGSAMIN_S2-v1.1.5_stats.txt
script: test/assert_txt.sh
- name: a_mini-collectwgsmetrics
message: test collectwgsmetrics
nf_script: main.nf
nf_config: test/config/cwm.config
params_file: test/yaml/a_mini.yaml
skip: true
verbose: true
asserts:
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_HG002.N_wgs-metrics.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_HG002.N_wgs-metrics.txt
script: test/assert_txt.sh
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Picard-*/output/Picard-*_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Picard-3.1.0_TWGSAMIN_S2-v1.1.5_wgs-metrics.txt
script: test/assert_txt.sh
- name: a_mini-bamqc
message: test bamqc
nf_script: main.nf
nf_config: test/config/bamqc.config
params_file: test/yaml/a_mini.yaml
skip: true
verbose: true
asserts:
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_HG002.N_stats/genome_results.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_HG002.N_stats/genome_results.txt
method: md5
- actual: generate-SQC-BAM-*/TWGSAMIN000001/Qualimap-*/output/Qualimap-*_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
expect: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-output/Qualimap-2.3_TWGSAMIN_S2-v1.1.5_stats/genome_results.txt
method: md5