From 801b68ab9603971311d808231ff31fa7e58af62a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 20:52:14 -0500
Subject: [PATCH] Remove explicit config and try replacing -bg with -q
---
.gitlab-ci.yml | 12 ++++++------
workflow/conf/biohpc_cluster.config | 6 +++---
2 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 85ce1e0..2eaaa76 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,7 +40,7 @@ simple_1:
- develop
- master
script:
- - nextflow -bg run workflow/main.nf -config 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'
+ - nextflow -q 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'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -64,7 +64,7 @@ simple_2:
- master
- tags
script:
- - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+ - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -87,7 +87,7 @@ detailed_1:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -config 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'
+ - nextflow -q 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'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -111,7 +111,7 @@ detailed_2:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+ - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -134,7 +134,7 @@ detailed_3:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -config 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'
+ - nextflow -q 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'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -157,7 +157,7 @@ detailed_4:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+ - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
artifacts:
name: "$CI_JOB_NAME"
when: always
diff --git a/workflow/conf/biohpc_cluster.config b/workflow/conf/biohpc_cluster.config
index 65b9862..d6c7087 100644
--- a/workflow/conf/biohpc_cluster.config
+++ b/workflow/conf/biohpc_cluster.config
@@ -5,7 +5,7 @@ process {
withLabel: checkDesignFile {
module = ['python/3.6.1-2-anaconda']
- executor = 'local'
+ queue = '32GB'
}
withLabel: count211 {
module = ['cellranger/2.1.1']
@@ -25,11 +25,11 @@ process {
}
withLabel: versions {
module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
- executor = 'local'
+ queue = '32GB'
}
withLabel: multiqc {
module = ['multiqc/1.7']
- executor = 'local'
+ queue = '32GB'
}
}
--
GitLab