update configs with better params

StaPH-B · May 12, 2020 · 2c4a466 · 2c4a466
1 parent eda87ff
commit 2c4a466
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Showing 8 changed files with 57 additions and 42 deletions.
diff --git a/packaging/setup.py b/packaging/setup.py
@@ -6,7 +6,7 @@
 
 setuptools.setup(
     name="staphb_toolkit",
-    version="1.0.0",
+    version="1.0.1",
     author="Kelsey Florek, Kevin Libuit",
     author_email="[email protected], [email protected]",
     description="A ToolKit of commonly used Public Health Bioinformatics Tools",

diff --git a/staphb_toolkit/workflows/dryad/configs/dryad_config_template.config b/staphb_toolkit/workflows/dryad/configs/dryad_config_template.config
@@ -9,14 +9,26 @@
 //####################
 //singularity.enabled = true
 //singularity.runOptions = ""
+//process.stageInMode = "link"
 
 //####################
 //##AWS Batch Params##
 //####################
+//process.executor = 'awsbatch'
+//process.queue = ''
 //aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 //aws.region = 'us-east-1'
 //workDir = 's3://'
-//cleanup=true
+
+//#######################
+//##Google Cloud Params##
+//#######################
+//process.executor = ''
+//google.project = ''
+//google.location = ''
+//google.region = ''
+//workDir = ''
+//google.lifeSciences.bootDiskSize = 50.GB
 
 //#########################
 //####Docker Containers####
@@ -69,10 +81,6 @@ params.cg_tree_model = "GTR+G"
 
 
 process {
-  //stageInMode = "link" //uncomment for singularity
-
-  //executor = 'awsbatch' //uncomment for AWS Batch
-  //queue = '' //uncomment for AWS Batch
 
   cpus = 2
   memory = '2 GB'

diff --git a/staphb_toolkit/workflows/foushee/configs/foushee_config_template.config b/staphb_toolkit/workflows/foushee/configs/foushee_config_template.config
@@ -9,14 +9,26 @@
 //####################
 //singularity.enabled = true
 //singularity.runOptions = ""
+//process.stageInMode = "link"
 
 //####################
 //##AWS Batch Params##
 //####################
+//process.executor = 'awsbatch'
+//process.queue = ''
 //aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 //aws.region = 'us-east-1'
 //workDir = 's3://'
-//cleanup=true
+
+//#######################
+//##Google Cloud Params##
+//#######################
+//process.executor = ''
+//google.project = ''
+//google.location = ''
+//google.region = ''
+//workDir = ''
+//google.lifeSciences.bootDiskSize = 50.GB
 
 //#########################
 //####Docker Containers####
@@ -63,10 +75,6 @@ params.kmer_snps = "-core"
 
 
 process {
-  //stageInMode = "link" //uncomment for singularity
-
-  //executor = 'awsbatch' //uncomment for AWS Batch
-  //queue = '' //uncomment for AWS Batch
 
   cpus = 2
   memory = '2 GB'

diff --git a/staphb_toolkit/workflows/monroe/configs/cluster_user_config.config b/staphb_toolkit/workflows/monroe/configs/cluster_user_config.config
@@ -9,22 +9,24 @@
 //####################
 //singularity.enabled = true
 //singularity.runOptions = ""
+//process.stageInMode = "link"
 
 //####################
 //##AWS Batch Params##
 //####################
+//process.executor = 'awsbatch'
+//process.queue = ''
 //aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 //aws.region = 'us-east-1'
 //workDir = 's3://'
-//cleanup=true
 
 //#######################
 //##Google Cloud Params##
 //#######################
+//process.executor = ''
 //google.project = ''
 //google.location = ''
 //google.region = ''
-//process.executor = ''
 //workDir = ''
 //google.lifeSciences.bootDiskSize = 50.GB
 
@@ -45,10 +47,6 @@ params.iqtree_model="GTR+G4"
 params.iqtree_boostraps=1000
 
 process {
-  //stageInMode = "link" //uncomment for singularity
-
-  //executor = 'awsbatch' //uncomment for AWS Batch
-  //queue = '' //uncomment for AWS Batch
 
   errorStrategy = 'retry'
   maxRetries = 1

diff --git a/staphb_toolkit/workflows/monroe/configs/ont_user_config.config b/staphb_toolkit/workflows/monroe/configs/ont_user_config.config
@@ -9,23 +9,25 @@
 //####################
 //singularity.enabled = true
 //singularity.runOptions = ""
+//process.stageInMode = "link"
 
 //####################
 //##AWS Batch Params##
 //####################
+//process.executor = 'awsbatch'
+//process.queue = ''
 //aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 //aws.region = 'us-east-1'
 //workDir = 's3://'
-//cleanup=true
-//gpu_queue = 'aws-nextflow-gpu' //Queue for GPU basecalling
+//process.withName.guppy_basecalling.queue = 'aws-nextflow-gpu' //Queue for GPU basecalling
 
 //#######################
 //##Google Cloud Params##
 //#######################
+//process.executor = ''
 //google.project = ''
 //google.location = ''
 //google.region = ''
-//process.executor = ''
 //workDir = ''
 //google.lifeSciences.bootDiskSize = 50.GB
 
@@ -62,18 +64,13 @@ params.polishing = "medaka" // polishing mode "nanopolish" or "medaka"
 params.normalise = 200
 
 process {
-  //stageInMode = "link" //uncomment for singularity
-
-  //executor = 'awsbatch' //uncomment for AWS Batch
-  //queue = '' //uncomment for AWS Batch
 
   cpus = 2
   memory = '2 GB'
 
   withName:guppy_basecalling{
     memory = '50 GB'
     cpus = 8
-    queue = gpu_queue
     container = guppy_gpu_container
   }
   withName:guppy_demultiplexing{

diff --git a/staphb_toolkit/workflows/monroe/configs/pe_user_config.config b/staphb_toolkit/workflows/monroe/configs/pe_user_config.config
@@ -9,22 +9,24 @@
 //####################
 //singularity.enabled = true
 //singularity.runOptions = ""
+//process.stageInMode = "link"
 
 //####################
 //##AWS Batch Params##
 //####################
+//process.executor = 'awsbatch'
+//process.queue = ''
 //aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 //aws.region = 'us-east-1'
 //workDir = 's3://'
-//cleanup=true
 
 //#######################
 //##Google Cloud Params##
 //#######################
+//process.executor = ''
 //google.project = ''
 //google.location = ''
 //google.region = ''
-//process.executor = ''
 //workDir = ''
 //google.lifeSciences.bootDiskSize = 50.GB
 
@@ -57,10 +59,6 @@ params.ivar_minfreq=0
 
 
 process {
-  //stageInMode = "link" //uncomment for singularity
-
-  //executor = 'awsbatch' //uncomment for AWS Batch
-  //queue = '' //uncomment for AWS Batch
 
   errorStrategy = 'retry'
   maxRetries = 1

diff --git a/staphb_toolkit/workflows/tredegar/configs/tredegar_config_template.config b/staphb_toolkit/workflows/tredegar/configs/tredegar_config_template.config
@@ -9,14 +9,26 @@
 //####################
 //singularity.enabled = true
 //singularity.runOptions = ""
+//process.stageInMode = "link"
 
 //####################
 //##AWS Batch Params##
 //####################
+//process.executor = 'awsbatch'
+//process.queue = ''
 //aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 //aws.region = 'us-east-1'
 //workDir = 's3://'
-//cleanup=true
+
+//#######################
+//##Google Cloud Params##
+//#######################
+//process.executor = ''
+//google.project = ''
+//google.location = ''
+//google.region = ''
+//workDir = ''
+//google.lifeSciences.bootDiskSize = 50.GB
 
 //#########################
 //####Docker Containers####
@@ -65,10 +77,6 @@ params.serotypefinder_agreement = "95.00"
 params.serotypefinder_coverage = "0.60"
 
 process {
-  //stageInMode = "link" //uncomment for singularity
-
-  //executor = 'awsbatch' //uncomment for AWS Batch
-  //queue = '' //uncomment for AWS Batch
 
   cpus = 2
   memory = '2 GB'

diff --git a/staphb_toolkit/workflows/universal_config_template.config b/staphb_toolkit/workflows/universal_config_template.config
@@ -9,22 +9,24 @@
 //####################
 //singularity.enabled = true
 //singularity.runOptions = ""
+//process.stageInMode = "link"
 
 //####################
 //##AWS Batch Params##
 //####################
+//process.executor = 'awsbatch'
+//process.queue = ''
 //aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
 //aws.region = 'us-east-1'
 //workDir = 's3://'
-//cleanup=true
 
 //#######################
 //##Google Cloud Params##
 //#######################
+//process.executor = ''
 //google.project = ''
 //google.location = ''
 //google.region = ''
-//process.executor = ''
 //workDir = ''
 //google.lifeSciences.bootDiskSize = 50.GB
 
@@ -40,10 +42,6 @@
 
 
 process {
-  //stageInMode = "link" //uncomment for singularity
-
-  //executor = 'awsbatch' //uncomment for AWS Batch
-  //queue = '' //uncomment for AWS Batch
 
   cpus = 2
   memory = '2 GB'