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Commit e84e13e8 authored by Venkat Malladi's avatar Venkat Malladi
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Resolve merge conflict.

parents 89d9e085 0817965e
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......@@ -6,6 +6,7 @@ before_script:
stages:
- unit
- skip
- single
- multiple
......@@ -62,3 +63,15 @@ paired_end_diff:
- pytest -m paireddiff
artifacts:
expire_in: 2 days
single_end_skip:
stage: skip
only:
- branches
except:
- master
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true -resume
- pytest -m singleskip_true
artifacts:
expire_in: 2 days
......@@ -17,9 +17,10 @@ params.cutoffRatio = 1.2
params.outDir= "$baseDir/output"
params.extendReadsLen = 100
params.topPeakCount = 600
params.skipDiff = false
params.skipMotif = false
params.references = "$baseDir/../docs/references.md"
// Check inputs
if( params.bwaIndex ){
bwaIndex = Channel
......@@ -47,6 +48,8 @@ cutoffRatio = params.cutoffRatio
outDir = params.outDir
extendReadsLen = params.extendReadsLen
topPeakCount = params.topPeakCount
skipDiff = params.skipDiff
skipMotif = params.skipMotif
references = params.references
// Check design file for errors
......@@ -440,6 +443,9 @@ process motifSearch {
file "*narrowPeak" into filteredPeaks
file('version_*.txt') into motifSearchVersions
when:
!skipMotif
script:
"""
......@@ -470,7 +476,7 @@ process diffPeaks {
file('version_*.txt') into diffPeaksVersions
when:
noUniqueExperiments > 1
noUniqueExperiments > 1 && !skipDiff
script:
"""
......
......@@ -19,6 +19,7 @@ def test_pie_singleend():
def test_upsetplot_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
@pytest.mark.singleend
def test_annotation_singleend():
annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
......
......@@ -10,14 +10,16 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/diffPeaks/'
@pytest.mark.singleend
@pytest.mark.singleskip_true
def test_diff_peaks_singleend_single_rep():
assert os.path.isdir(test_output_path) == False
@pytest.mark.pairedend
def test_diff_peaks_pairedend_single_rep():
assert os.path.isdir(test_output_path) == False
@pytest.mark.singlediff
def test_heatmap_singleend_multiple_rep():
assert os.path.exists(os.path.join(test_output_path, 'heatmap.pdf'))
......
......@@ -23,13 +23,18 @@ def test_motif_search_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html'))
@pytest.mark.singleskip_true
def test_motif_search_singleend():
assert os.path.isdir(test_output_path) == False
@pytest.mark.pairedend
def test_limited_peaks_pairedend():
peak_file_ENCSR729LGA= test_output_path + 'ENCSR729LGA.600.narrowPeak'
assert os.path.exists(peak_file_ENCSR729LGA)
assert utils.count_lines(peak_file_ENCSR729LGA) == 600
@pytest.mark.pairedend
def test_motif_search_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'ENCSR729LGA.fa'))
......
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