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' -- GitLab