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 -- GitLab