From c17b8a62e4275d1c5547b79468d490d6c0b2fb3a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 22 Apr 2020 13:45:10 -0500
Subject: [PATCH] Add unit CI test for (new) inferMetadata
---
.gitlab-ci.yml | 33 ++++++++++++++++++++++------
workflow/rna-seq.nf | 2 +-
workflow/tests/test_dataQC.py | 14 ++++++++++++
workflow/tests/test_inferMetadata.py | 2 +-
4 files changed, 42 insertions(+), 9 deletions(-)
create mode 100644 workflow/tests/test_dataQC.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a4417f8..ae5a8ed 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -35,6 +35,24 @@ parseMetadata:
- singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded
- singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species
+inferMetadata:
+ stage: unit
+ script:
+ - >
+ align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5JA_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%'))
+ if [[ ${align} == "" ]]
+ then
+ exit 1
+ fi
+ - >
+ singularity run 'docker://bicf/rseqc3.0:2.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam" 1>> Q-Y5JA_1M.se.inferMetadata.log
+ ended=`bash inferMeta.sh endness Q-Y5JA_1M.se.inferMetadata.log
+ if [[ ${ended} == "" ]]
+ then
+ exit 1
+ fi
+ - pytest -m inferMetadata
+
getRef:
stage: unit
script:
@@ -73,20 +91,20 @@ dedupData:
echo "samtools view -b Q-Y5JA_1M.se.sorted.deduped.bam ${i} > Q-Y5JA_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5JA_1M.se.sorted.deduped.${i}.bam Q-Y5JA_1M.se.sorted.deduped.${i}.bam.bai;";
done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j 20 -k
- pytest -m dedupData
-
-makeBigWig:
- stage: unit
- script:
- - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o Q-Y5JA_1M.se.bw
- - pytest -m makeBigWig
-makeFeatureCounts:
+ countData:
stage: unit
script:
- singularity run 'docker://bicf/subread2:2.0.0' featureCounts -R SAM -p -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -T 20 -s 1 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -o Q-Y5JA_1M.se.featureCounts -g 'gene_name' --primary --ignoreDup -B ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam
- singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5JA_1M.se.featureCounts
- pytest -m makeFeatureCounts
+makeBigWig:
+ stage: unit
+ script:
+ - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5JA_1M.se.sorted.deduped.bam -o Q-Y5JA_1M.se.bw
+ - pytest -m makeBigWig
+
fastqc:
stage: unit
script:
@@ -106,6 +124,7 @@ downsampleData:
- singularity exec 'docker://bicf/seqtk:2.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz 1000 1> sampled.1.fq
- pytest -m downsampleData
+
integration_se:
stage: integration
script:
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 9412658..03816c1 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -437,7 +437,7 @@ process inferMetadata {
# infer experimental setting from dedup bam
echo "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.err
- infer_experiment.py -r "\${bed}" -i "\${bam}" > ${repRID}.inferMetadata.log 2>> ${repRID}.inferMetadata.err
+ infer_experiment.py -r "\${bed}" -i "\${bam}" 1>> ${repRID}.inferMetadata.log 2>> ${repRID}.inferMetadata.err
echo "LOG: determining endedness and strandedness from file" >> ${repRID}.inferMetadata.err
ended=`bash inferMeta.sh endness ${repRID}.inferMetadata.log` 1>> ${repRID}.inferMetadata.out 2>> ${repRID}.inferMetadata.err
diff --git a/workflow/tests/test_dataQC.py b/workflow/tests/test_dataQC.py
new file mode 100644
index 0000000..95eb332
--- /dev/null
+++ b/workflow/tests/test_dataQC.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+ '/../../'
+
+@pytest.mark.dataQC
+def test_dataQC():
+ assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.se.sorted.deduped.tin.xls'))
+
diff --git a/workflow/tests/test_inferMetadata.py b/workflow/tests/test_inferMetadata.py
index 44ffbc3..f2908be 100644
--- a/workflow/tests/test_inferMetadata.py
+++ b/workflow/tests/test_inferMetadata.py
@@ -10,5 +10,5 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.inferMetadata
def test_inferMetadata():
- assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.se.sorted.deduped.tin.xls'))
+ assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.se.inferMetadata.log'))
--
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