Fix merge of tests.

workflow/main.nf

@@ -38,6 +38,7 @@ readsList = Channel
 pairedEnd = params.pairedEnd
 designFile = params.designFile
 genomeSize = params.genomeSize
+genome = params.genome
 chromSizes = params.chromSizes
 fasta = params.fasta
 cutoffRatio = params.cutoffRatio
@@ -422,6 +423,7 @@ process motifSearch {
   output:
 
   file "*memechip" into motifSearch
+  file "sorted-*" into filteredPeaks
 
   script:
 

workflow/scripts/annotate_peaks.R

@@ -21,16 +21,16 @@ if (length(args) != 2) {
 }
 
 design_file <- args[1]
-genome <-args[2]
+genome_assembly <- args[2]
 
 # Load UCSC Known Genes
-if(genome=='GRCh37') {
+if(genome_assembly=='GRCh37') {
     txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
     annodb <- 'org.Hs.eg.db'
-} else if(genome=='GRCm38')  {
+} else if(genome_assembly=='GRCm38')  {
     txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
     annodb <- 'org.Mm.eg.db'
-} else if(genome=='GRCh38')  {
+} else if(genome_assembly=='GRCh38')  {
     txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
     annodb <- 'org.Hs.eg.db'
 }

workflow/tests/test_annotate_peaks.py

@@ -16,7 +16,7 @@ def test_annotate_peaks_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
     annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.csv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 149820
+    assert utils.count_lines(annotation_file) == 152840
 
 
 @pytest.mark.pairedend

workflow/tests/test_call_peaks_macs.py

@@ -13,7 +13,7 @@ def test_call_peaks_macs_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
     peak_file = test_output_path + 'ENCLB144FDT_peaks.narrowPeak'
-    assert utils.count_lines(peak_file) == 210349
+    assert utils.count_lines(peak_file) == 227389
 
 
 @pytest.mark.pairedend

workflow/tests/test_diff_peaks.py

@@ -12,20 +12,11 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.singleend
 def test_diff_peaks_singleend_single_rep():
-    assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.bed'))
-    assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.csv'))
-    assert os.path.exists(os.path.join(test_output_path, 'no_heatmap.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'no_pca.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.pdf'))
-
+    assert os.path.isdir(test_output_path) == False
 
 @pytest.mark.pairedend
 def test_annotate_peaks_pairedend_single_rep():
-    assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.bed'))
-    assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.csv'))
-    assert os.path.exists(os.path.join(test_output_path, 'no_heatmap.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'no_pca.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.pdf'))
+    assert os.path.isdir(test_output_path) == False
 
 @pytest.mark.singlediff
 def test_diff_peaks_singleend_multiple_rep():

workflow/tests/test_overlap_peaks.py

@@ -37,7 +37,7 @@ def test_check_update_design(design_diff):
 def test_overlap_peaks_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
     peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
-    assert utils.count_lines(peak_file) == 150302
+    assert utils.count_lines(peak_file) == 149828
 
 
 @pytest.mark.pairedend

workflow/tests/test_trim_reads.py

@@ -24,7 +24,7 @@ def test_trim_reads_singleend():
 @pytest.mark.pairedend
 def test_trim_reads_pairedend():
     raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
-    trimmed_fastq = test_output_path + ' ENCLB637LZP_val_2.fq.gz'
+    trimmed_fastq = test_output_path + 'ENCFF582IOZ_val_2.fq.gz'
     trimmed_fastq_report = test_output_path + \
                             'ENCLB637LZP.fastq.gz_trimming_report.txt'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)

workflow/tests/test_xcor.py

@@ -9,13 +9,13 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 
 @pytest.mark.singleend
-def test_convert_reads_singleend():
+def test_map_qc_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.plot.pdf'))
     qc_file = os.path.join(test_output_path,"ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.qc")
     df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
-    assert df_xcor[2].iloc[0] == '195,215,230'
-    assert df_xcor[8].iloc[0] == 1.024836
-    assert df_xcor[9].iloc[0] == 1.266678
+    assert df_xcor[2].iloc[0] == '190,200,210'
+    assert df_xcor[8].iloc[0] == 1.025906
+    assert df_xcor[9].iloc[0] == 1.139671
 
 
 @pytest.mark.pairedend
@@ -23,6 +23,6 @@ def test_map_qc_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCFF582IOZ_val_2ENCFF957SQS_val_1.filt.nodup.tagAlign.15.tagAlign.gz.cc.plot.pdf'))
     qc_file = os.path.join(test_output_path,"ENCFF582IOZ_val_2ENCFF957SQS_val_1.filt.nodup.tagAlign.15.tagAlign.gz.cc.qc")
     df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
-    assert df_xcor[2].iloc[0] == '205,410,430'
-    assert df_xcor[8].iloc[0] == 1.060266
-    assert df_xcor[9].iloc[0] == 4.308793
+    assert df_xcor[2].iloc[0] == '210,220,475'
+    assert df_xcor[8].iloc[0] == 1.062032
+    assert df_xcor[9].iloc[0] == 3.737722