Merge branch '31-skip_steps' into 'master'

Resolve "skip motif search and diff bind"

Closes #31

See merge request !21

.gitlab-ci.yml

@@ -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

workflow/main.nf

@@ -17,6 +17,8 @@ params.cutoffRatio = 1.2
 params.outDir= "$baseDir/output"
 params.extendReadsLen = 100
 params.topPeakCount = 600
+params.skipDiff = false
+params.skipMotif = false
 
 // Check inputs
 if( params.bwaIndex ){
@@ -45,6 +47,8 @@ cutoffRatio = params.cutoffRatio
 outDir = params.outDir
 extendReadsLen = params.extendReadsLen
 topPeakCount = params.topPeakCount
+skipDiff = params.skipDiff
+skipMotif = params.skipMotif
 
 // Check design file for errors
 process checkDesignFile {
@@ -427,6 +431,9 @@ process motifSearch {
   file "*memechip" into motifSearch
   file "*narrowPeak" into filteredPeaks
 
+  when:
+  !skipMotif
+
   script:
 
   """
@@ -456,7 +463,7 @@ process diffPeaks {
   file 'normcount_peaksets.txt' into normCountPeaks
 
   when:
-  noUniqueExperiments > 1
+  noUniqueExperiments > 1 && !skipDiff
 
   script:
   """

workflow/tests/test_annotate_peaks.py

@@ -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'

workflow/tests/test_diff_peaks.py

@@ -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'))

workflow/tests/test_motif_search.py

@@ -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'))