Commit 42d20250 authored by van den Berg's avatar van den Berg
Browse files

Shorten test names

parent ea8629eb
Pipeline #4079 failed with stages
in 7 minutes and 29 seconds
- name: test-dry-run
- name: dry-run-vanilla
tags:
- dry-run
command: >
......@@ -21,7 +21,7 @@
must_not_contain:
- rror
- name: test-dry-run-target-baits
- name: dry-run-target-baits
tags:
- dry-run
command: >
......@@ -40,7 +40,7 @@
must_not_contain:
- rror
- name: test-bed-coverage-dry-run
- name: dry-run-bed-coverage
tags:
- dry-run
command: >
......
- name: test-integration-no-cluster
- name: integration-vanilla
tags:
- integration
command: >
......@@ -47,7 +47,7 @@
- picard_AlignmentSummaryMetrics
- picard_DuplicationMetrics
- name: test-integration-small-scatter
- name: integration-small-scatter
tags:
- integration
command: >
......@@ -85,7 +85,7 @@
- path: micro/vcf/micro.0.vcf.gz.tbi
should_exist: false
- name: test-integration-refflat
- name: integration-refflat
tags:
- integration
command: >
......@@ -100,7 +100,7 @@
must_not_contain:
- rror
- name: test-integration-all-on-target
- name: integration-all-on-target
tags:
- integration
command: >
......@@ -126,7 +126,7 @@
- "sample_name\tpreqc_reads\tpreqc_bases\tpostqc_reads\tpostqc_bases\tmapped_reads\tmapped_bases\tmedian_coverage"
- "micro\t15440\t2276743\t15440\t2274413\t15424\t2262944\t136"
- name: test-integration-gene-bedfile
- name: integration-gene-bedfile
tags:
- integration
command: >
......@@ -146,7 +146,7 @@
- "sample_name\tpreqc_reads\tpreqc_bases\tpostqc_reads\tpostqc_bases\tmapped_reads\tmapped_bases\tmedian_coverage"
- "micro\t15440\t2276743\t15440\t2274413\t15424\t2262944\t133.0"
- name: test-integration-two-known-sites
- name: integration-two-known-sites
tags:
- integration
command: >
......@@ -164,7 +164,7 @@
must_not_contain:
- rror
- name: test-integration-two-readgroups
- name: integration-two-readgroups
tags:
- integration
command: >
......@@ -203,7 +203,7 @@
- lib_01
- lib_02
- name: test-integration-two-samples
- name: integration-two-samples
tags:
- integration
command: >
......@@ -236,7 +236,7 @@
- '"sample_name": "micro1",'
- '"sample_name": "micro2",'
- name: test-integration-target-baits
- name: integration-target-baits
tags:
- integration
command: >
......@@ -252,7 +252,7 @@
- BAIT_SET
- FOLD_80_BASE_PENALTY
- name: test-integration-bed-coverage
- name: integration-bed-coverage
tags:
- integration
command: >
......@@ -285,7 +285,7 @@
contains:
- "(null)\t0\t0"
- name: test-integration-restrict-BQSR
- name: integration-restrict-BQSR
tags:
- integration
command: >
......
- name: test-no-reference
- name: sanity-no-reference
tags:
- sanity
command: >
......@@ -9,7 +9,7 @@
contains:
- 'Invalid --configfile: ''reference'' is a required property'
- name: test-reference-does-not-exist
- name: sanity-reference-does-not-exist
tags:
- sanity
command: >
......@@ -21,13 +21,13 @@
- Missing input files for rule align
- /this/file/is/not/there
- name: test-snakemake
- name: sanity-snakemake
tags:
- sanity
command: |
snakemake --version
- name: test-singluarity-version
- name: sanity-singularity
tags:
- sanity
command: |
......@@ -36,7 +36,7 @@
contains:
- singularity version 3
- name: test-baits-only
- name: sanity-baits-only
tags:
- sanity
command: >
......@@ -47,7 +47,7 @@
contains:
- 'Invalid --configfile: "baitsfile" specified without "targetsfile"'
- name: test-samples-overlapping-name
- name: sanity-samples-overlapping-name
tags:
- sanity
command: >
......@@ -58,7 +58,7 @@
contains:
- 'Invalid --configfile: sample names should not overlap ("micro1" is contained in "micro12")'
- name: snakemake-lint
- name: sanity-snakemake-lint
tags:
- sanity
command: >
......
......@@ -6,14 +6,14 @@ import pytest
import os
@pytest.mark.workflow('test-integration-no-cluster')
@pytest.mark.workflow('integration-vanilla')
def test_stats_file_exists(workflow_dir):
stats_file = 'stats.tsv'
full_path = workflow_dir / pathlib.Path(stats_file)
assert os.path.exists(full_path)
@pytest.mark.workflow('test-integration-no-cluster')
@pytest.mark.workflow('integration-vanilla')
def test_stats_file_name(workflow_dir):
""" Read in the stats file and do some tests """
stats_file = 'stats.tsv'
......@@ -27,7 +27,7 @@ def test_stats_file_name(workflow_dir):
assert data['sample_name'] == 'micro'
@pytest.mark.workflow('test-integration-no-cluster')
@pytest.mark.workflow('integration-vanilla')
def test_stats_file_mapped_reads(workflow_dir):
""" Read in the stats file and do some tests """
stats_file = 'stats.tsv'
......@@ -41,7 +41,7 @@ def test_stats_file_mapped_reads(workflow_dir):
assert data['mapped_reads'] == '15424'
@pytest.mark.workflow('test-integration-no-cluster')
@pytest.mark.workflow('integration-vanilla')
def test_stats_file_mapped_bases(workflow_dir):
""" Read in the stats file and do some tests """
stats_file = 'stats.tsv'
......@@ -55,7 +55,7 @@ def test_stats_file_mapped_bases(workflow_dir):
assert data['mapped_bases'] == '2262944'
@pytest.mark.workflow('test-integration-no-cluster')
@pytest.mark.workflow('integration-vanilla')
def test_stats_file_preqc_reads(workflow_dir):
""" Read in the stats file and do some tests """
stats_file = 'stats.tsv'
......@@ -69,7 +69,7 @@ def test_stats_file_preqc_reads(workflow_dir):
assert data['preqc_reads'] == '15440'
@pytest.mark.workflow('test-integration-no-cluster')
@pytest.mark.workflow('integration-vanilla')
def test_stats_file_preqc_bases(workflow_dir):
""" Read in the stats file and do some tests """
stats_file = 'stats.tsv'
......
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