Add unit test for makeFeatureCounts

.gitlab-ci.yml

@@ -77,6 +77,13 @@ makeBigWig:
   - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p `nproc` -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o Q-Y5JA_1M.se.bw
   - pytest -m makeBigWig
 
+makeFeatureCounts:
+  stage: unit
+  script:
+  - singularity run 'docker://bicf/bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T `nproc` -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam 
+  - singularity run 'docker://bicf/bicf/subread2:2.0.0' Rscript calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
+  - pytest -m makeFeatureCounts
+
 fastqc:
   stage: unit
   script:

workflow/rna-seq.nf

@@ -362,31 +362,7 @@ process dedupData {
 }
 
 /*
- *fastqc: run fastqc on untrimmed fastq's
-*/
-process fastqc {
-  tag "${repRID}"
-  publishDir "${outDir}/fastqc", mode: 'copy', pattern: "*_fastqc.zip"
-  publishDir "${logsDir}", mode: 'copy', pattern: "*.fastq.err"
-
-  input:
-    path (fastq) from fastqs_fastqc
-
-  output:
-    path ("*_fastqc.zip") into fastqc
-
-  script:
-    """
-    hostname >${repRID}.fastqc.err
-    ulimit -a >>${repRID}.fastqc.err
-
-    # run fastqc
-    fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
-    """
-}
-
-/*
- *Make BigWig files for later processes
+ *makeBigWig: make bigwig file
 */
 process makeBigWig {
   tag "${repRID}"
@@ -405,7 +381,7 @@ process makeBigWig {
 }
 
 /*
- *Run featureCounts and get the counts, tpm, and fpkm
+ *Run featureCounts and get the counts, tpm
 */
 process makeFeatureCounts {
   tag "${repRID}"
@@ -426,3 +402,28 @@ process makeFeatureCounts {
     Rscript calculateTPM.R --count "${repRID}.featureCounts"
     """
 }
+
+
+/*
+ *fastqc: run fastqc on untrimmed fastq's
+*/
+process fastqc {
+  tag "${repRID}"
+  publishDir "${outDir}/fastqc", mode: 'copy', pattern: "*_fastqc.zip"
+  publishDir "${logsDir}", mode: 'copy', pattern: "*.fastq.err"
+
+  input:
+    path (fastq) from fastqs_fastqc
+
+  output:
+    path ("*_fastqc.zip") into fastqc
+
+  script:
+    """
+    hostname >${repRID}.fastqc.err
+    ulimit -a >>${repRID}.fastqc.err
+
+    # run fastqc
+    fastqc *.fastq.gz -o . >>${repRID}.fastqc.err
+    """
+}

workflow/tests/test_makeFeatureCounts.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+import os
+import utils
+
+data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+	'/../../'
+
+
+@pytest.mark.makeFeatureCounts
+def test_makeFeatureCounts():
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.featureCounts'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA_1M.se.countTable.csv'))