From 17fe1fd5e603d52c1c5f56ac4cab7b0ba0742791 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 21:06:45 -0500
Subject: [PATCH] Revert to layered configs
---
.gitlab-ci.yml | 12 +--
.../{biohpc_local.config => biohpc.config} | 26 ------
workflow/conf/biohpc_cluster.config | 88 -------------------
workflow/conf/cluster.config | 31 +++++++
workflow/conf/local.config | 25 ++++++
workflow/nextflow.config | 11 ++-
6 files changed, 69 insertions(+), 124 deletions(-)
rename workflow/conf/{biohpc_local.config => biohpc.config} (71%)
mode change 100755 => 100644
delete mode 100644 workflow/conf/biohpc_cluster.config
create mode 100644 workflow/conf/cluster.config
create mode 100755 workflow/conf/local.config
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b33b296..c0a034f 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -40,7 +40,7 @@ simple_1:
- develop
- master
script:
- - 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'
+ - 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'
- pytest -m count310
artifacts:
name: "$CI_JOB_NAME"
@@ -65,7 +65,7 @@ simple_2:
- master
- tags
script:
- - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+ - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
- pytest -m count310
artifacts:
name: "$CI_JOB_NAME"
@@ -89,7 +89,7 @@ detailed_1:
refs:
- tags
script:
- - 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'
+ - 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'
- pytest -m count310
artifacts:
name: "$CI_JOB_NAME"
@@ -114,7 +114,7 @@ detailed_2:
refs:
- tags
script:
- - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+ - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
- pytest -m count302
artifacts:
name: "$CI_JOB_NAME"
@@ -138,7 +138,7 @@ detailed_3:
refs:
- tags
script:
- - 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'
+ - 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'
- pytest -m count301
artifacts:
name: "$CI_JOB_NAME"
@@ -162,7 +162,7 @@ detailed_4:
refs:
- tags
script:
- - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+ - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
- pytest -m count211
artifacts:
name: "$CI_JOB_NAME"
diff --git a/workflow/conf/biohpc_local.config b/workflow/conf/biohpc.config
old mode 100755
new mode 100644
similarity index 71%
rename from workflow/conf/biohpc_local.config
rename to workflow/conf/biohpc.config
index 182f03b..7304219
--- a/workflow/conf/biohpc_local.config
+++ b/workflow/conf/biohpc.config
@@ -1,29 +1,3 @@
-process {
- executor = 'local'
-
- withLabel: checkDesignFile {
- module = ['python/3.6.1-2-anaconda']
- }
- withLabel: count211 {
- module = ['cellranger/2.1.1']
- }
- withLabel: count301 {
- module = ['cellranger/3.0.1']
- }
- withLabel: count302 {
- module = ['cellranger/3.0.2']
- }
- withLabel: count310 {
- module = ['cellranger/3.1.0']
- }
- withLabel: versions {
- module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
- }
- withLabel: multiqc {
- module = ['multiqc/1.7']
- }
-}
-
params {
// Reference file paths on BioHPC
genomes {
diff --git a/workflow/conf/biohpc_cluster.config b/workflow/conf/biohpc_cluster.config
deleted file mode 100644
index d6c7087..0000000
--- a/workflow/conf/biohpc_cluster.config
+++ /dev/null
@@ -1,88 +0,0 @@
-process {
- executor = 'slurm'
- queue = '32GB'
- clusterOptions = '--hold'
-
- withLabel: checkDesignFile {
- module = ['python/3.6.1-2-anaconda']
- queue = '32GB'
- }
- withLabel: count211 {
- module = ['cellranger/2.1.1']
- queue = '128GB,256GB,256GBv1,384GB'
- }
- withLabel: count301 {
- module = ['cellranger/3.0.1']
- queue = '128GB,256GB,256GBv1,384GB'
- }
- withLabel: count302 {
- module = ['cellranger/3.0.2']
- queue = '128GB,256GB,256GBv1,384GB'
- }
- withLabel: count310 {
- module = ['cellranger/3.1.0']
- queue = '128GB,256GB,256GBv1,384GB'
- }
- withLabel: versions {
- module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
- queue = '32GB'
- }
- withLabel: multiqc {
- module = ['multiqc/1.7']
- queue = '32GB'
- }
-}
-
-params {
- // Reference file paths on BioHPC
- genomes {
- 'GRCh38-3.0.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'GRCh38-1.2.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'hg19-3.0.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'hg19-1.2.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'mm10-3.0.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'mm10-1.2.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'GRCh38_and_mm10-3.1.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'hg19_and_mm10-3.0.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'hg19_and_mm10-1.2.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- 'ercc92-1.2.0' {
- loc = '/project/apps_database/cellranger/refdata-cellranger-'
- }
- }
- // Chemistry mapping parameter
- chemistry {
- 'auto' {
- param = 'auto'
- }
- '3GEXv1' {
- param = 'SC3Pv1'
- }
- '3GEXv2' {
- param = 'SC3Pv2'
- }
- '3GEXv3' {
- param = 'SC3Pv3'
- }
- '5GEX' {
- param = 'fiveprime'
- }
- }
-}
diff --git a/workflow/conf/cluster.config b/workflow/conf/cluster.config
new file mode 100644
index 0000000..2526210
--- /dev/null
+++ b/workflow/conf/cluster.config
@@ -0,0 +1,31 @@
+process {
+ executor = 'slurm'
+ queue = '32GB'
+ clusterOptions = '--hold'
+
+ withLabel: checkDesignFile {
+ module = ['python/3.6.1-2-anaconda']
+ }
+ withLabel: count211 {
+ module = ['cellranger/2.1.1']
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: count301 {
+ module = ['cellranger/3.0.1']
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: count302 {
+ module = ['cellranger/3.0.2']
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: count310 {
+ module = ['cellranger/3.1.0']
+ queue = '128GB,256GB,256GBv1,384GB'
+ }
+ withLabel: versions {
+ module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
+ }
+ withLabel: multiqc {
+ module = ['multiqc/1.7']
+ }
+}
diff --git a/workflow/conf/local.config b/workflow/conf/local.config
new file mode 100755
index 0000000..556476f
--- /dev/null
+++ b/workflow/conf/local.config
@@ -0,0 +1,25 @@
+process {
+ executor = 'local'
+
+ withLabel: checkDesignFile {
+ module = ['python/3.6.1-2-anaconda']
+ }
+ withLabel: count211 {
+ module = ['cellranger/2.1.1']
+ }
+ withLabel: count301 {
+ module = ['cellranger/3.0.1']
+ }
+ withLabel: count302 {
+ module = ['cellranger/3.0.2']
+ }
+ withLabel: count310 {
+ module = ['cellranger/3.1.0']
+ }
+ withLabel: versions {
+ module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
+ }
+ withLabel: multiqc {
+ module = ['multiqc/1.7']
+ }
+}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 527b3ca..1cfa59d 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -1,9 +1,12 @@
profiles {
- biohpc_local {
- includeConfig 'conf/biohpc_local.config'
+ biohpc {
+ includeConfig 'conf/biohpc.config'
}
- biohpc_cluster {
- includeConfig 'conf/biohpc_cluster.config'
+ local {
+ includeConfig 'conf/local.config'
+ }
+ cluster {
+ includeConfig 'conf/cluster.config'
}
aws {
includeConfig 'conf/aws.config'
--
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