From 85e6ed53d1857cfea0fbf71bb3d0b61868baee39 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 20:29:38 -0500
Subject: [PATCH] Compress profile configs
---
.gitlab-ci.yml | 12 +++----
workflow/conf/biohpc_cluster.config | 54 ++++++++++++++++++++++++++++
workflow/conf/biohpc_local.config | 56 ++++++++++++++++++++++++++++-
workflow/nextflow.config | 7 ++--
4 files changed, 117 insertions(+), 12 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b1c8e35..85ce1e0 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 -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'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -64,7 +64,7 @@ simple_2:
- master
- tags
script:
- - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+ - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
artifacts:
name: "$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 -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'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -111,7 +111,7 @@ detailed_2:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+ - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
artifacts:
name: "$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 -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'
artifacts:
name: "$CI_JOB_NAME"
when: always
@@ -157,7 +157,7 @@ detailed_4:
refs:
- tags
script:
- - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+ - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
artifacts:
name: "$CI_JOB_NAME"
when: always
diff --git a/workflow/conf/biohpc_cluster.config b/workflow/conf/biohpc_cluster.config
index 9fe87af..65b9862 100644
--- a/workflow/conf/biohpc_cluster.config
+++ b/workflow/conf/biohpc_cluster.config
@@ -32,3 +32,57 @@ process {
executor = 'local'
}
}
+
+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/biohpc_local.config b/workflow/conf/biohpc_local.config
index 0eb72d4..182f03b 100755
--- a/workflow/conf/biohpc_local.config
+++ b/workflow/conf/biohpc_local.config
@@ -22,4 +22,58 @@ process {
withLabel: multiqc {
module = ['multiqc/1.7']
}
-}
\ No newline at end of file
+}
+
+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/nextflow.config b/workflow/nextflow.config
index 863af3c..94688ff 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -1,11 +1,8 @@
profiles {
- biohpc {
- includeConfig 'conf/biohpc.config'
- }
- local {
+ biohpc.local {
includeConfig 'conf/biohpc_local.config'
}
- cluster {
+ biohpc.cluster {
includeConfig 'conf/biohpc_cluster.config'
}
aws {
--
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