From 416b482a01c9658f1e7410d3c81b5eecca6b7d0a Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Thu, 4 Feb 2021 14:40:48 +0000
Subject: [PATCH] Fix config

---
 nextflow.config | 9 +++++----
 workflow.nf     | 2 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 3cedce5..d70566b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -4,11 +4,12 @@
 // The workflow should run without editing this configuration file,
 // however there may be instances in which you wish to edit this
 // file for compute performance or other reasons. Please see:
-// 
+//
 //   https://nextflow.io/docs/latest/config.html#configuration
 //
 // for further help editing this file.
 
+
 profiles {
     // the "standard" profile is used implicitely by nextflow
     // if no other profile is given on the CLI
@@ -20,12 +21,12 @@ profiles {
             runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
         }
         process {
-            withLabel:default {
+            withLabel:pysam {
                 container = 'workflow-template:latest'
             }
         }
     }
-
+    
     // profile using conda environments rather than docker
     // containers
     conda {
@@ -33,7 +34,7 @@ profiles {
             enabled = false
         }
         process {
-            withLabel:default {
+            withLabel:pysam {
                 conda = "environment.yaml"
             }
         }
diff --git a/workflow.nf b/workflow.nf
index 82e6e26..ba5a33f 100644
--- a/workflow.nf
+++ b/workflow.nf
@@ -32,7 +32,7 @@ if(params.help) {
 
 process readSeqs {
     // Just write a file with sequence lengths
-    label "default"
+    label "pysam"
     input:
         file reads
     output: