From 3da0fb063143be32840c9e0c94b937b7e92175a9 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 14 Jul 2020 16:38:13 -0500
Subject: [PATCH] Fix new CI unit tests
---
.gitlab-ci.yml | 2 +-
workflow/scripts/createTestData.sh | 11 +++++++++++
2 files changed, 12 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 17a81a9..4be9f97 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -68,7 +68,7 @@ trimData:
downsampleData:
stage: unit
script:
- - singularity exec 'docker://bicf/seqtk:2.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M_trimmed.fq.gz 1000 1> sampled.1.fq
+ - singularity exec 'docker://bicf/seqtk:2.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
- pytest -m downsampleData
alignData:
diff --git a/workflow/scripts/createTestData.sh b/workflow/scripts/createTestData.sh
index 752d1ab..2b76481 100644
--- a/workflow/scripts/createTestData.sh
+++ b/workflow/scripts/createTestData.sh
@@ -51,6 +51,8 @@ singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrnam
singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
+cp Q-Y5F6_1M.se.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.se.bam
+cp Q-Y5F6_1M.pe.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.pe.bam
cp Q-Y5F6_1M.se.sorted.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.bam
cp Q-Y5F6_1M.se.sorted.bam.bai ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.bam.bai
cp Q-Y5F6_1M.pe.sorted.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.pe.sorted.bam
@@ -58,6 +60,14 @@ cp Q-Y5F6_1M.pe.sorted.bam.bai ./NEW_test_data/bam/small/Q-Y5F6_1M.pe.sorted.bam
cp Q-Y5F6_1M.se.alignSummary.txt ./NEW_test_data/meta/Q-Y5F6_1M.se.alignSummary.txt
cp Q-Y5F6_1M.pe.alignSummary.txt ./NEW_test_data/meta/Q-Y5F6_1M.pe.alignSummary.txt
+singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
+singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.deduped.bam
+singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai
+cp Q-Y5F6_1M.se.sorted.deduped.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
+cp Q-Y5F6_1M.se.sorted.deduped.bam.bai ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam.bai
+cp Q-Y5F6_1M.se.deduped.Metrics.txt /NEW_test_data/meta/Q-Y5F6_1M.se.deduped.Metrics.txt
+cp Q-Y5F6_1M.se.deduped.Metrics.txt ./NEW_test_data/meta/Q-Y5F6_1M.se.deduped.Metrics.txt
+
for i in {"chr8","chr4","chrY"}; do
echo "samtools view -b ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam ${i} > Q-Y5F6_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.${i}.bam Q-Y5F6_1M.se.sorted.deduped.${i}.bam.bai;";
done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j 20 -k
@@ -72,6 +82,7 @@ mkdir -p ./NEW_test_data/counts
mkdir -p ./NEW_test_data/counts/small
singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' -o Q-Y5F6_1M.se.featureCounts -s 1 -R SAM --primary --ignoreDup ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count Q-Y5F6_1M.se.featureCounts
+cp Q-Y5F6_1M.se.featureCounts ./NEW_test_data/counts/small/Q-Y5F6_1M.se.featureCounts
cp Q-Y5F6_1M.se.countTable.csv ./NEW_test_data/counts/small/Q-Y5F6_1M.se.countTable.csv
mkdir -p ./NEW_test_data/bw
--
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