.gitlab-ci.yml

before_script:
  - echo "before script"
  - export PATH="$HOME/.local/cmake-3.23.0-rc1-linux-x86_64/bin:$HOME/.cargo/bin:$PATH"

after_script:
  - echo "after script"

stages:
  - build_d
  - build_r
  - test_0
  - test_1
  - test_2

build_debug:
  stage: build_d
  script:
    - echo "Build for debug"
    - pwd
    - export
    - cd src_o; make clean; make debug
    - mv debug ../software
    - pwd
  artifacts:
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 4 yrs
    paths:
    - software

build_release:
  stage: build_r
  script:
    - echo "Build for release"
    - pwd
    - cd src_o; make clean; make release
    - mv release ../software
    - pwd
  artifacts:
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 4 yrs
    paths:
    - software
  dependencies:
    - build_debug


HCC1187_10X_0_1_noise_20:
  stage: test_0
  script:
    - input_dir=/y/hlab/AccurityTestData/HCC1187/mixed_sample/
    - cna_truth_file=/y/hlab/AccurityTestData/HCC1187/hcc1187_truth.tsv
    - true_purity=0.1
    - output_dir=HCC1187_10X_0_1_noise_20
    - echo "Test ${output_dir}";
    - pwd; ls
    - test/test_tcga.py -f ${input_dir}
      --segment_stddev_divider 20 -t purity_${true_purity} -n normal_5X -c 4
      -o ${output_dir} -w pyflow
    - ./src_o/plotCPandMCP.py -t ${cna_truth_file}
      -r /y/hlab/AccurityTestData/hs38d1/genome.dict
      -i ${output_dir}/cnv.output.tsv
      -o ${output_dir}/plot.cnv.vs.true.purity${true_purity}.png
    - test/judge_result.py -i ${output_dir}/infer.out.tsv -u 0.077 -d 2.7
  needs: ["build_debug"]
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - HCC1187_10X_0_1_noise_20/
  dependencies:
    - build_debug

HCC1187_10X_0_3_noise_10:
  stage: test_1
  script:
    - echo "Test HCC1187_10X_0.3_noise_10";
    - pwd
    - test/test_tcga.py -f /y/hlab/AccurityTestData/HCC1187/mixed_sample/ -t purity_0.3 -n normal_5X -c 4 -o HCC1187_10X_0_3_noise_10 -w pyflow
    - test/judge_result.py -i HCC1187_10X_0_3_noise_10/infer.out.tsv -u 0.241 -d 2.7
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - HCC1187_10X_0_3_noise_10/
  dependencies:
    - build_debug


HCC1187_10X_0_4_noise_10:
  stage: test_1
  script:
    - echo "Test HCC1187_10X_0.4_noise_10";
    - pwd
    - test/test_tcga.py -f /y/hlab/AccurityTestData/HCC1187/mixed_sample/ -t purity_0.4 -n normal_5X -c 4 -o HCC1187_10X_0_4_noise_10 -w pyflow
    - test/judge_result.py -i HCC1187_10X_0_4_noise_10/infer.out.tsv -u 0.331 -d 2.7
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - HCC1187_10X_0_4_noise_10/
  dependencies:
    - build_debug

HCC1187_10X_0_6_noise_20:
  stage: test_1
  script:
    - echo "Test HCC1187_10X_0.6 noise 20";
    - pwd
    - test/test_tcga.py -f /y/hlab/AccurityTestData/HCC1187/mixed_sample/ -t purity_0.6 -n normal_5X -c 4 -o HCC1187_10X_0_6_noise_20 -w pyflow
    - test/judge_result.py -i HCC1187_10X_0_6_noise_20/infer.out.tsv -u 0.526 -d 2.7
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - HCC1187_10X_0_6_noise_20/
  dependencies:
    - build_debug

HCC1187_10X_0_6:
  stage: test_1
  script:
    - echo "Test HCC1187_10X_0.6";
    - pwd
    - test/test_tcga.py -f /y/hlab/AccurityTestData/HCC1187/mixed_sample/ -t purity_0.6 -n normal_5X -c 4 -o HCC1187_10X_0_6 -w pyflow
    - test/judge_result.py -i HCC1187_10X_0_6/infer.out.tsv -u 0.526 -d 2.7
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - HCC1187_10X_0_6/
  dependencies:
    - build_debug

SNP_HCC1187_10X_0_6:
  stage: test_2
  script:
    - echo "Test H1187_10X purity=0.6 call SNPs, 20 cores";
    - pwd
    - test/test_tcga.py -f /y/hlab/AccurityTestData/HCC1187/mixed_sample/ -t purity_0.6 -n normal_5X -c 20 --call_snps -o HCC1187_10X_0_6 -w pyflow
    - test/judge_result.py -i HCC1187_10X_0_6/infer.out.tsv -u 0.526 -d 2.7
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - HCC1187_10X_0_6/
  dependencies:
    - build_debug

HCC1187_10X_0_9:
  stage: test_2
  script:
    - echo "Test HCC1187_10X_0.9";
    - pwd
    - test/test_tcga.py -f /y/hlab/AccurityTestData/HCC1187/mixed_sample/ -t purity_0.9 -n normal_5X -c 4 -o HCC1187_10X_0_9 -w pyflow
    - test/judge_result.py -i HCC1187_10X_0_9/infer.out.tsv -u 0.87 -d 2.7
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - HCC1187_10X_0_9/
  dependencies:
    - build_debug

#tcga40X_574_580_06_5411_noise_20:
#  stage: test_2
#  script:
#    - echo "Test reduce noise 20 574_580_TCGA-06-5411_Broad_GSC_vs_1_by_method5_realigned0_reduced0";
#    - pwd
#    - test/test_tcga.py -f /y/Sunset/db/individual_alignment/ -t 574_580_TCGA-06-5411_Broad_GSC_vs_1_by_method5_realigned0_reduced0 -n 578_586_TCGA-06-5411_Broad_GSC_vs_1_by_method5_realigned0_reduced0 -c 4 -o 40X_574_580_06_5411_Broad_noise_20 -w pyflow
#    - test/judge_result.py -i 40X_574_580_06_5411_Broad_noise_20/infer.out.tsv -u 0.6 -d 2.5 --max_purity_delta 0.3 --max_ploidy_delta 1.3
#  artifacts:
#    when: always
#    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
#    expire_in: 12 mos
#    paths:
#    - 40X_574_580_06_5411_Broad_noise_20/
#  dependencies:
#    - build_debug
#
#tcga40X_574_580_06_5411_Broad:
#  stage: test_2
#  script:
#    - echo "Test 574_580_TCGA-06-5411_Broad_GSC_vs_1_by_method5_realigned0_reduced0";
#    - pwd
#    - test/test_tcga.py -f /y/Sunset/db/individual_alignment/ -t 574_580_TCGA-06-5411_Broad_GSC_vs_1_by_method5_realigned0_reduced0 -n 578_586_TCGA-06-5411_Broad_GSC_vs_1_by_method5_realigned0_reduced0 -c 4 -o 40X_574_580__06_5411_Broad -w pyflow
#    - test/judge_result.py -i 40X_574_580__06_5411_Broad/infer.out.tsv -u 0.6 -d 2.5 --max_purity_delta 0.3 --max_ploidy_delta 1.3
#  artifacts:
#    when: always
#    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
#    expire_in: 12 mos
#    paths:
#    - 40X_574_580__06_5411_Broad/
#  dependencies:
#    - build_debug

tcga35X_586_595_19_2624_noise_20:
  stage: test_1
  script:
    - echo "Test reduce noise 20 on 586_595_TCGA-19-2624_Broad_GSC_vs_1_by_method5_realigned0_reduced0";
    - pwd
    - test/test_tcga.py -f /y/Sunset/db/individual_alignment/ -t 586_595_TCGA-19-2624_Broad_GSC_vs_1_by_method5_realigned0_reduced0 -n 602_611_TCGA-19-2624_Broad_GSC_vs_1_by_method5_realigned0_reduced0 -c 4 -o 35X_586_595_19_2624_Broad_noise_20 -w pyflow
    - test/judge_result.py -i 35X_586_595_19_2624_Broad_noise_20/infer.out.tsv -u 0.94571 -d 1.89 --max_purity_delta 0.1 --max_ploidy_delta 0.3
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - 35X_586_595_19_2624_Broad_noise_20/
  dependencies:
    - build_debug

#tcga35X_586_595_19_2624_Broad:
#  stage: test_2
#  script:
#    - echo "Test 586_595_TCGA-19-2624_Broad_GSC_vs_1_by_method5_realigned0_reduced0";
#    - pwd
#    - test/test_tcga.py -f /y/Sunset/db/individual_alignment/ -t 586_595_TCGA-19-2624_Broad_GSC_vs_1_by_method5_realigned0_reduced0 -n 602_611_TCGA-19-2624_Broad_GSC_vs_1_by_method5_realigned0_reduced0 -c 4 -o 35X_586_595__19_2624_Broad -w pyflow
#    - test/judge_result.py -i 35X_586_595__19_2624_Broad/infer.out.tsv -u 0.85 -d 2.0 --max_purity_delta 0.1 --max_ploidy_delta 0.3
#  artifacts:
#    when: always
#    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
#    expire_in: 12 mos
#    paths:
#    - 35X_586_595__19_2624_Broad/
#  dependencies:
#    - build_debug

tcga7X_1590_96__AO_AOJJ_HMS:
  stage: test_0
  script:
    - echo "Test 1590_96_TCGA-AO-A0JJ_HMS_CGCC_vs_633_by_method5_realigned0_reduced0";
    - pwd
    - test/test_tcga.py -r hs38d1 -f /y/Sunset/db/individual_alignment/
      -t 1590_96_TCGA-AO-A0JJ_HMS_CGCC_vs_633_by_method5_realigned0_reduced0
      -n 1574_80_TCGA-AO-A0JJ_HMS_CGCC_vs_633_by_method5_realigned0_reduced0
      -c 4 -o 7X_1590_96__AO_AOJJ_HMS -w pyflow
    - test/judge_result.py -i 7X_1590_96__AO_AOJJ_HMS/infer.out.tsv -u 0.50245
      -d 1.9693 --max_purity_delta 0.3 --max_ploidy_delta 1
  needs: ["build_debug"]
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - 7X_1590_96__AO_AOJJ_HMS/
  dependencies:
    - build_debug

tcga7X_1590_96_AO_AOJJ_noise_20:
  stage: test_1
  script:
    - echo "Test noise reduce 20 on 1590_96_TCGA-AO-A0JJ_HMS_CGCC_vs_633_by_method5_realigned0_reduced0";
    - pwd
    - test/test_tcga.py -r hs38d1 -f /y/Sunset/db/individual_alignment/ -t 1590_96_TCGA-AO-A0JJ_HMS_CGCC_vs_633_by_method5_realigned0_reduced0 -n 1574_80_TCGA-AO-A0JJ_HMS_CGCC_vs_633_by_method5_realigned0_reduced0 -c 4 -o 7X_1590_96_AO_AOJJ_HMS_noise_20 -w pyflow
    - test/judge_result.py -i 7X_1590_96_AO_AOJJ_HMS_noise_20/infer.out.tsv -u 0.50491 -d 1.9745 --max_purity_delta 0.3 --max_ploidy_delta 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - 7X_1590_96_AO_AOJJ_HMS_noise_20/
  dependencies:
    - build_debug

tcga3X_1125_431_AA_3968:
  stage: test_1
  script:
    - echo "Test 1125_431_TCGA-AA-3968_HMS_CGCC_vs_1_by_method5_realigned0_reduced0";
    - pwd
    - test/test_tcga.py -f /y/Sunset/db/individual_alignment/ -t 1125_431_TCGA-AA-3968_HMS_CGCC_vs_1_by_method5_realigned0_reduced0 -n 1117_422_TCGA-AA-3968_HMS_CGCC_vs_1_by_method5_realigned0_reduced0 -c 4 -o 3X_1125_431__AA_3968_HMS -w pyflow
    - test/judge_result.py -i 3X_1125_431__AA_3968_HMS/infer.out.tsv -u 0.55417 -d 2.1484 --max_purity_delta 0.1 --max_ploidy_delta 0.3
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - 3X_1125_431__AA_3968_HMS
  dependencies:
    - build_debug

tcga3X_1125_431_AA_3968_divider_20:
  stage: test_1
  script:
    - echo "Test noise divider 20 on 1125_431_TCGA-AA-3968_HMS_CGCC_vs_1_by_method5_realigned0_reduced0";
    - pwd
    - test/test_tcga.py -f /y/Sunset/db/individual_alignment/ -t 1125_431_TCGA-AA-3968_HMS_CGCC_vs_1_by_method5_realigned0_reduced0 -n 1117_422_TCGA-AA-3968_HMS_CGCC_vs_1_by_method5_realigned0_reduced0 -c 4 -o 3X_1125_431_AA_3968_HMS_divider20 -w pyflow
    - test/judge_result.py -i 3X_1125_431_AA_3968_HMS_divider20/infer.out.tsv -u 0.60518 -d 2.0896 --max_purity_delta 0.1 --max_ploidy_delta 0.3
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - 3X_1125_431_AA_3968_HMS_divider20
  dependencies:
    - build_debug

singleclone_5x_0_1_noise_20:
  stage: test_2
  script:
    - echo "singleclone_5x 0.1 reduce noise 20";
    - pwd
    - test/test_simulation.py -y singleclone_5x -p 0.1 -c 4 -o pyflow.log --debug 1
    - test/judge_simulation_result.sh singleclone_5x 1 0
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - singleclone_5x/purity.*/infer_result_debug
    - singleclone_5x/result*.tsv
  dependencies:
    - build_debug

singleclone_5x_0_5:
  stage: test_1
  script:
    - echo "singleclone_5x 0.5";
    - pwd
    - test/test_simulation.py -y singleclone_5x -p 0.5 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh singleclone_5x 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - singleclone_5x/purity.*/infer_result_debug
    - singleclone_5x/result*.tsv
  dependencies:
    - build_debug

singleclone_5x_0_5_noise_20:
  stage: test_2
  script:
    - echo "singleclone_5x 0.5 reduce noise 20";
    - pwd
    - test/test_simulation.py -y singleclone_5x -p 0.5 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh singleclone_5x 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - singleclone_5x/purity.*/infer_result_debug
    - singleclone_5x/result*.tsv
  dependencies:
    - build_debug


singleclone_5x_0_9:
  stage: test_2
  script:
    - echo "singleclone_5x 0.9";
    - pwd
    - test/test_simulation.py -y singleclone_5x -p 0.9 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh singleclone_5x 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - singleclone_5x/purity.*/infer_result_debug
    - singleclone_5x/result*.tsv
  dependencies:
    - build_debug

singleclone_1percSNP_0_1:
  stage: test_2
  script:
    - echo "singleclone_1_of_100snp 0.1";
    - pwd
    - test/test_simulation.py -y singleclone_1_of_100snp -p 0.1 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh singleclone_1_of_100snp 1 0
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - singleclone_1_of_100snp/purity.*/infer_result_debug
    - singleclone_1_of_100snp/result*.tsv
  dependencies:
    - build_debug

singleclone_1percSNP_0_5:
  stage: test_2
  script:
    - echo "singleclone_1_of_100snp 0.5";
    - pwd
    - test/test_simulation.py -y singleclone_1_of_100snp -p 0.5 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh singleclone_1_of_100snp 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - singleclone_1_of_100snp/purity.*/infer_result_debug
    - singleclone_1_of_100snp/result*.tsv
  dependencies:
    - build_debug

singleclone_1percSNP_0_9:
  stage: test_2
  script:
    - echo "singleclone_1_of_100snp 0.9";
    - pwd
    - test/test_simulation.py -y singleclone_1_of_100snp -p 0.9 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh singleclone_1_of_100snp 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - singleclone_1_of_100snp/purity.*/infer_result_debug
    - singleclone_1_of_100snp/result*.tsv
  dependencies:
    - build_debug


subclone_2_0_1_noise_20:
  stage: test_2
  script:
    - echo "subclone_2 0.1 reduce noise 20";
    - pwd
    - test/test_simulation.py -y subclone_2 -p 0.1 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh subclone_2 1 0
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - subclone_2/purity.*/infer_result_debug
    - subclone_2/result*.tsv
  dependencies:
    - build_debug

subclone_2_0_5_noise_20:
  stage: test_2
  script:
    - echo "subclone_2 0.5 reduce noise 20";
    - pwd
    - test/test_simulation.py -y subclone_2 -p 0.5 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh subclone_2 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - subclone_2/purity.*/infer_result_debug
    - subclone_2/result*.tsv
  dependencies:
    - build_debug

subclone_2_0_5:
  stage: test_2
  script:
    - echo "subclone_2 0.5";
    - pwd
    - test/test_simulation.py -y subclone_2 -p 0.5 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh subclone_2 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - subclone_2/purity.*/infer_result_debug
    - subclone_2/result*.tsv
  dependencies:
    - build_debug

SNP_subclone_2_0_5:
  stage: test_2
  script:
    - echo "subclone_2 0.5 call_snps 20 cores";
    - pwd
    - test/test_simulation.py -y subclone_2 -p 0.5 -c 20 --call_snps -o pyflow --debug 1
    - test/judge_simulation_result.sh subclone_2 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - subclone_2/purity.*/infer_result_debug
    - subclone_2/result*.tsv
  dependencies:
    - build_debug


subclone_3_0_5:
  stage: test_2
  script:
    - echo "subclone_3 0.5";
    - pwd
    - test/test_simulation.py -y subclone_3 -p 0.5 -c 4 -o pyflow --debug 1
    - test/judge_simulation_result.sh subclone_3 1 1
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - subclone_3/purity.*/infer_result_debug
    - subclone_3/result*.tsv
  dependencies:
    - build_debug

#WGD_purity_0_7:
#  stage: test_2
#  script:
#    - echo "WGD purity 0.7";
#    - pwd
#    - test/test_simulation.py -y WGD_purity0.7 -p 0.7 -c 4 -o pyflow --debug 1
#    - test/judge_simulation_result.sh WGD_purity0.7
#  artifacts:
#    when: always
#    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
#    expire_in: 12 mos
#    paths:
#    - WGD_purity0.7/purity.*/infer_result_debug
#    - WGD_purity0.7/result*.tsv
#  dependencies:
#    - build_debug
#
#WGD_purity_divider_20:
#  stage: test_2
#  script:
#    - echo "WGD purity 0.7 noise reduce 20";
#    - pwd
#    - test/test_simulation.py -y WGD_purity0.7 -p 0.7 -c 4 -o pyflow --debug 1
#    - test/judge_simulation_result.sh WGD_purity0.7
#  artifacts:
#    when: always
#    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
#    expire_in: 12 mos
#    paths:
#    - WGD_purity0.7/purity.*/infer_result_debug
#    - WGD_purity0.7/result*.tsv
#  dependencies:
#    - build_debug

5M_single_mutant_0_7:
  stage: test_1
  script:
    - echo "5M_single_mutant 0.7";
    - pwd
    - test/test_simulation.py -y 5M_single_mutant -p 0.7 -c 4 -o pyflow --debug 1
    - test/judge_result.py -i 5M_single_mutant/purity.0.7/infer_result_debug/infer.out.tsv -u 0.7 -d 2.0 --max_purity_delta 0.1 --max_ploidy_delta 0.2
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - 5M_single_mutant/purity.*/infer_result_debug
    - 5M_single_mutant/result*.tsv
  dependencies:
    - build_debug

5M_single_mutant_0_7_release:
  stage: test_1
  script:
    - echo "5M_single_mutant 0.7 release";
    - pwd
    - test/test_simulation.py -y 5M_single_mutant -p 0.7 -c 4 -o pyflow --debug 0
    - test/judge_result.py -i 5M_single_mutant/purity.0.7/infer_result_debug/infer.out.tsv -u 0.7 -d 2.0 --max_purity_delta 0.1 --max_ploidy_delta 0.2
  artifacts:
    when: always
    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
    expire_in: 12 mos
    paths:
    - 5M_single_mutant/purity.*/infer_result_debug
    - 5M_single_mutant/result*.tsv
  dependencies:
    - build_release

#collect:
#  stage: collect_result
#  script:
#    - echo "collect_result";
#    - pwd
#    - test/collect_result.sh
#  artifacts:
#    name: "${CI_JOB_ID}_${CI_JOB_NAME}_${CI_COMMIT_REF_NAME}"
#    expire_in: 4 yrs
#    paths:
#    - run_result_png



#job_clean:
#  stage: cleanup
#  script:
#    - pwd
#    - ls src_o
#    - echo "clean"
#  dependencies:
#    - build_debug