From 09cb56b3615cdec244743d931824f4da1d46639d Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Fri, 21 Feb 2020 11:32:50 -0600 Subject: [PATCH] Fix nextflow config layering problem --- workflow/conf/aws.config | 4 ++++ workflow/conf/aws_ondemand.config | 9 --------- workflow/conf/aws_spot.config | 9 --------- workflow/conf/aws_user.config | 9 --------- workflow/conf/biohpc.config | 24 ------------------------ workflow/conf/biohpc_cluster.config | 7 +++++++ workflow/conf/biohpc_local.config | 22 ++++++++++++++++++++++ workflow/nextflow.config | 9 --------- 8 files changed, 33 insertions(+), 60 deletions(-) delete mode 100755 workflow/conf/aws_ondemand.config delete mode 100755 workflow/conf/aws_spot.config delete mode 100644 workflow/conf/aws_user.config diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config index 7794329..6875c65 100644 --- a/workflow/conf/aws.config +++ b/workflow/conf/aws.config @@ -1,11 +1,15 @@ +workDir = 's3://' aws.client.storageEncryption = 'AES256' aws { + region = '' batch { cliPath = '/home/ec2-user/miniconda/bin/aws' } } process { + executor = 'awsbatch' + queue = 'default-' cpus = 1 memory = '10 GB' } \ No newline at end of file diff --git a/workflow/conf/aws_ondemand.config b/workflow/conf/aws_ondemand.config deleted file mode 100755 index d12c2de..0000000 --- a/workflow/conf/aws_ondemand.config +++ /dev/null @@ -1,9 +0,0 @@ -workDir = 's3:// -aws { - region = 'us-east-2' -} - -process { - executor = 'awsbatch' - queue = 'highpriority-' -} \ No newline at end of file diff --git a/workflow/conf/aws_spot.config b/workflow/conf/aws_spot.config deleted file mode 100755 index 0a81a79..0000000 --- a/workflow/conf/aws_spot.config +++ /dev/null @@ -1,9 +0,0 @@ -workDir = 's3://' -aws { - region = 'us-east-2' -} - -process { - executor = 'awsbatch' - queue = 'default-' -} \ No newline at end of file diff --git a/workflow/conf/aws_user.config b/workflow/conf/aws_user.config deleted file mode 100644 index 68dd2f5..0000000 --- a/workflow/conf/aws_user.config +++ /dev/null @@ -1,9 +0,0 @@ -workDir = 's3://' -aws { - region = '' -} - -process { - executor = 'awsbatch' - queue = '' -} \ No newline at end of file diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config index eb1fc5c..bdcc3c4 100755 --- a/workflow/conf/biohpc.config +++ b/workflow/conf/biohpc.config @@ -1,27 +1,3 @@ -process { - 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 index 789d1e9..bebd64a 100644 --- a/workflow/conf/biohpc_cluster.config +++ b/workflow/conf/biohpc_cluster.config @@ -4,24 +4,31 @@ process { clusterOptions = '--hold' withLabel: checkDesignFile { + module = ['python/3.6.1-2-anaconda'] executor = 'local' } 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'] executor = 'local' } withLabel: multiqc { + module = ['multiqc/1.7'] executor = 'local' } } \ No newline at end of file diff --git a/workflow/conf/biohpc_local.config b/workflow/conf/biohpc_local.config index 9ca703b..0eb72d4 100755 --- a/workflow/conf/biohpc_local.config +++ b/workflow/conf/biohpc_local.config @@ -1,3 +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'] + } } \ No newline at end of file diff --git a/workflow/nextflow.config b/workflow/nextflow.config index f1a8650..9496393 100644 --- a/workflow/nextflow.config +++ b/workflow/nextflow.config @@ -11,15 +11,6 @@ profiles { aws { includeConfig 'conf/aws.config' } - ondemand { - includeConfig 'conf/aws_ondemand.config' - } - spot { - includeConfig 'conf/aws_spot.config' - } - awsUserDefined { - includeConfig 'conf/aws_user.config' - } } trace { -- GitLab