From 5f7f3d0f31d60af360f2a1fe812f98ede961c5df Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 13 Sep 2017 17:06:47 -0500
Subject: [PATCH] Add gitlab-ci test configuration and update testing.
---
.gitlab-ci.yml | 8 ++++++++
astrocyte_pkg.yml | 13 +++++++++----
test_data/fetch_test_data.sh | 2 ++
workflow/main.nf | 2 +-
4 files changed, 20 insertions(+), 5 deletions(-)
create mode 100644 .gitlab-ci.yml
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..8a2a5ef
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,8 @@
+before_script:
+ - sh test_data/fetch_test_data.sh
+
+test:
+ script:
+ - module add astrocyte/0.1.0
+ - cd ..
+ - astrocyte_cli test chipseq_analysis
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 7baf3cc..b812c4a 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -17,7 +17,8 @@ title: 'BICF ChIP-seq Analysis Workflow'
# A summary of the workflow package in plain text
description: |
This is a workflow package for the BioHPC/BICF ChIP-seq workflow system.
- It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker and MEME-ChIP, visualization application.
+ It implements a simple ChIP-seq analysis workflow and
+ visualization application.
# -----------------------------------------------------------------------------
# DOCUMENTATION
@@ -91,7 +92,11 @@ workflow_parameters:
- [ 'true', 'True']
- [ 'false', 'False']
description: |
- In single-end sequencing, the sequencer reads a fragment from only one end to the other, generating the sequence of base pairs. In paired-end reading it starts at one read, finishes this direction at the specified read length, and then starts another round of reading from the opposite end of the fragment.
+ In single-end sequencing, the sequencer reads a fragment from only one
+ end to the other, generating the sequence of base pairs. In paired-end
+ reading it starts at one read, finishes this direction at the specified
+ read length, and then starts another round of reading from the opposite
+ end of the fragment.
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
@@ -109,8 +114,8 @@ vizapp_cran_packages:
- shiny
- shinyFiles
-# # List of any Bioconductor packages, not provided by the modules, that must be made
-# available to the vizapp
+# List of any Bioconductor packages, not provided by the modules,
+# that must be made available to the vizapp
vizapp_bioc_packages:
- qusage
# - ballgown
diff --git a/test_data/fetch_test_data.sh b/test_data/fetch_test_data.sh
index c47fcf0..31c3b8f 100644
--- a/test_data/fetch_test_data.sh
+++ b/test_data/fetch_test_data.sh
@@ -1,2 +1,4 @@
+echo "Downloading test set..."
wget -O ENCLB904PZW_R1.fastq.gz https://www.encodeproject.org/files/ENCFF704XKC/@@download/ENCFF704XKC.fastq.gz
wget -O ENCLB904PZW_R2.fastq.gz https://www.encodeproject.org/files/ENCFF707CNX/@@download/ENCFF707CNX.fastq.gz
+echo "Done"
diff --git a/workflow/main.nf b/workflow/main.nf
index a43afe5..1777855 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -3,7 +3,7 @@
// Path to an input file, or a pattern for multiple inputs
// Note - $baseDir is the location of this workflow file main.nf
-params.reads = "$baseDir/../test_data/*_{1,2}.fastq.gz"
+params.reads = "$baseDir/../test_data/*_R{1,2}.fastq.gz"
params.singleEnd = false
--
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