From 62642c4d9dfc6cc748cbc4f7fef7d0d4ef074c99 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 20:21:08 -0500
Subject: [PATCH] Add nexflow.config to ci run
---
.gitlab-ci.yml | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 3fd9c99..739a342 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,7 +40,7 @@ simple_1:
- develop
- master
script:
- - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+ - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -64,7 +64,7 @@ simple_2:
- master
- tags
script:
- - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+ - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -87,7 +87,7 @@ detailed_1:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
+ - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -111,7 +111,7 @@ detailed_2:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+ - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -134,7 +134,7 @@ detailed_3:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
+ - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -157,7 +157,7 @@ detailed_4:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+ - nextflow -bg run workflow/main.nf -C workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
artifacts:
name: "$CI_JOB_NAME"
when: always
--
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