Running with gitlab-runner 12.9.0 (4c96e5ad)
  on astrocyte-pipeline-tester qAESZL-b
section_start:1596205985:prepare_executor
Preparing the "shell" executor
Using Shell executor...
section_end:1596205985:prepare_executor
section_start:1596205985:prepare_script
Preparing environment
Running on Nucleus009...
section_end:1596205985:prepare_script
section_start:1596205985:get_sources
Getting source from Git repository
Fetching changes...
Initialized empty Git repository in /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/7751/100344/.git/
Created fresh repository.
From https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis
 * [new ref]         refs/pipelines/7751 -> refs/pipelines/7751
 * [new branch]      36-UpdateNextflow -> origin/36-UpdateNextflow
 * [new branch]      dev        -> origin/dev
 * [new branch]      master     -> origin/master
 * [new tag]         publish_1.0.0 -> publish_1.0.0
 * [new tag]         publish_2.0.3 -> publish_2.0.3
 * [new tag]         publish_2.0.4rc1 -> publish_2.0.4rc1
Checking out 66c9f064 as dev...
Removing .tmp/
Skipping Git submodules setup
section_end:1596205997:get_sources
section_start:1596205997:restore_cache
Restoring cache
section_end:1596205997:restore_cache
section_start:1596205997:download_artifacts
Downloading artifacts
section_end:1596205997:download_artifacts
section_start:1596205997:build_script
Running before_script and script
$ module add  python/3.6.1-2-anaconda
$ pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
Requirement already satisfied: pytest-pythonpath==0.7.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (0.7.1)
Requirement already satisfied: pytest-cov==2.5.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (2.5.1)
Requirement already satisfied: pytest>=2.5.2 in /cm/shared/apps/python/3.6.1-2-anaconda/lib/python3.6/site-packages (from pytest-pythonpath==0.7.1) (3.0.7)
Requirement already satisfied: coverage>=3.7.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest-cov==2.5.1) (4.5.2)
Requirement already satisfied: py>=1.4.29 in /cm/shared/apps/python/3.6.1-2-anaconda/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (1.4.33)
Requirement already satisfied: setuptools in /cm/shared/apps/python/3.6.1-2-anaconda/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (40.6.2)
You are using pip version 18.1, however version 20.2b1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
$ module load  nextflow/0.31.0
$ ln -s /project/shared/bicf_workflow_ref/workflow_testdata/atacseq/*fastq.gz test_data/
$ pytest -m unit --cov=./workflow/scripts
============================= test session starts ==============================
platform linux -- Python 3.6.1, pytest-3.0.7, py-1.4.33, pluggy-0.4.0
rootdir: /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/7751/100344, inifile: pytest.ini
plugins: pythonpath-0.7.1, cov-2.5.1
collected 58 items

workflow/tests/test_check_design.py .........
workflow/tests/test_overlap_peaks.py .
workflow/tests/test_pool_and_psuedoreplicate.py ..
workflow/tests/test_utils.py ......

----------- coverage: platform linux, python 3.6.1-final-0 -----------
Name                                           Stmts   Miss  Cover
------------------------------------------------------------------
workflow/scripts/atac_qc.py                       86     86     0%
workflow/scripts/call_peaks_macs.py              123    123     0%
workflow/scripts/check_design.py                 117     37    68%
workflow/scripts/convert_reads.py                 68     68     0%
workflow/scripts/experiment_design.py             28     15    46%
workflow/scripts/experiment_qc.py                141    114    19%
workflow/scripts/frip.py                          39     39     0%
workflow/scripts/generate_references.py           27     27     0%
workflow/scripts/generate_versions.py             63     63     0%
workflow/scripts/map_qc.py                       151    151     0%
workflow/scripts/map_reads.py                    150    150     0%
workflow/scripts/overlap_peaks.py                111     85    23%
workflow/scripts/pool_and_psuedoreplicate.py     137    113    18%
workflow/scripts/trim_reads.py                    72     72     0%
workflow/scripts/utils.py                         77     36    53%
workflow/scripts/xcor.py                          68     68     0%
------------------------------------------------------------------
TOTAL                                           1458   1247    14%


============================= 40 tests deselected ==============================
================== 18 passed, 40 deselected in 15.03 seconds ===================
section_end:1596206039:build_script
section_start:1596206039:after_script
Running after_script
section_end:1596206039:after_script
section_start:1596206039:archive_cache
Saving cache
section_end:1596206039:archive_cache
section_start:1596206039:upload_artifacts_on_success
Uploading artifacts for successful job
section_end:1596206039:upload_artifacts_on_success
Job succeeded