From 529dadea0b6b1599c7161156f0d301b11f3fb192 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 30 Jan 2020 13:17:07 -0600
Subject: [PATCH] Cleanup some ci misses
---
.gitignore | 2 +-
.gitlab-ci.yml | 2 +-
workflow/rna-seq.nf | 3 +--
workflow/tests/test_alignReads.py | 18 ++++++++----------
4 files changed, 11 insertions(+), 14 deletions(-)
diff --git a/.gitignore b/.gitignore
index 9b75a20..f86b65e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -298,4 +298,4 @@ timeline*.html*
*.out
run*.sh
-!.gitkeep
+!.gitkeep
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3dbf06e..f25142b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -51,7 +51,7 @@ trimData:
alignData:
stage: unit
script:
- - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz
+ - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam
- singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bai
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 46abbf1..6c3622b 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -234,7 +234,7 @@ process getRef {
*/
process trimData {
tag "${repRID}"
- publishDir "${logsDir}", mode: "copy", pattern: "${repRID}.trimData.*"
+ publishDir "${logsDir}", mode: "copy", pattern: "*.trimData.*"
input:
val endsManual_trimData
@@ -266,7 +266,6 @@ process trimData {
*/
process alignData {
tag "${repRID}"
- publishDir "${outDir}/alignData", mode: "copy", pattern: "*.{bam,bai}"
publishDir "${logsDir}", mode: "copy", pattern: "*.align.{out,err}"
input:
diff --git a/workflow/tests/test_alignReads.py b/workflow/tests/test_alignReads.py
index 74507ee..7c20dd3 100644
--- a/workflow/tests/test_alignReads.py
+++ b/workflow/tests/test_alignReads.py
@@ -7,8 +7,6 @@ import utils
data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
-logs_output_path = os.path.dirname(os.path.abspath(__file__)) + \
- '/../../'
@pytest.mark.alignData
@@ -27,15 +25,15 @@ def test_alignData_pe():
@pytest.mark.alignLogs
def test_alignLogs_se():
- assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.err'))
- assert '34497376 reads; of these:' in open(os.path.join(logs_output_path, '16-1ZX4.align.err')).readlines()[0]
- assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.out'))
+ assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.align.err'))
+ assert '34497376 reads; of these:' in open(os.path.join(data_output_path, '16-1ZX4.align.err')).readlines()[0]
+ assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.align.out'))
@pytest.mark.alignLogs
def test_alignLogs_pe():
- assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.err'))
- assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.err')) == 7
- assert '15824858 reads; of these:' in open(os.path.join(logs_output_path, 'Q-Y5JA.align.err')).readlines()[0]
- assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.out'))
- assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.out')) == 0
+ assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.align.err'))
+ assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.align.err')) == 7
+ assert '15824858 reads; of these:' in open(os.path.join(data_output_path, 'Q-Y5JA.align.err')).readlines()[0]
+ assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.align.out'))
+ assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.align.out')) == 0
--
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