From 0411ae5d7ca7418e2d0fa8eb2d71565b0852a419 Mon Sep 17 00:00:00 2001
From: Mihaela Zavolan <mihaela.zavolan@unibas.ch>
Date: Wed, 24 Nov 2021 11:44:04 +0100
Subject: [PATCH] Added nextflow installation test
---
.gitlab-ci.yml | 8 ++++++--
main.nf | 34 ++++++++++++++++++++++++++++++++++
2 files changed, 40 insertions(+), 2 deletions(-)
create mode 100755 main.nf
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 24e6cbf..28d51c4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -11,7 +11,7 @@ qc_1:
- pip install -r requirements.txt
- pip install -r requirements_dev.txt
- pip install -e .
-
+
script:
- flake8 src/ setup.py
- coverage run --source src/ -m pytest
@@ -25,7 +25,11 @@ test_1:
- pip install -r requirements.txt
- pip install -r requirements_dev.txt
- pip install -e .
+ - apt update -y
+ - apt install wget -y
+ - wget -qO- https://get.nextflow.io | bash
+ - nextflow self-update
script:
- - python -m pytest
+ - nextflow main.nf
diff --git a/main.nf b/main.nf
new file mode 100755
index 0000000..a740ba1
--- /dev/null
+++ b/main.nf
@@ -0,0 +1,34 @@
+/*
+ * pipeline input parameters
+ */
+params.annoFile = "$baseDir/inputs/ref_annotation.gt"
+params.copyNr = "$baseDir/inputs/transcript_tpms.txt"
+params.outdir = "results"
+
+log.info """\
+ R N A S E Q - N F P I P E L I N E
+ ===================================
+ annotation : ${params.annoFile}
+ copy numbers: ${params.copyNr}
+ output dir : ${params.outdir}
+ """
+ .stripIndent()
+
+
+/*
+ * check that input files are there
+ */
+process mock {
+
+ input:
+ path annoFile from params.annoFile
+ path copyNr from params.copyNr
+
+ script:
+ """
+ echo "Checked $annoFile and $copyNr"
+ """
+
+}
+
+
--
GitLab