🔥🍏 Remove duplicate standard slurm profiles

.readthedocs.yaml

@@ -4,9 +4,19 @@
 # Required
 version: 2
 
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.9"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
+
+# install dependencies using requirements file
+python:
+  install:
+    - requirements: docs/requirements.txt

docs/requirements.txt

@@ -0,0 +1,3 @@
+sphinx==4.2.0
+sphinx_rtd_theme==1.0.0
+readthedocs-sphinx-search==0.1.1

modules/local/diamond_blastp.nf

@@ -8,7 +8,7 @@ process DIAMOND_BLASTP {
     tag "Aligning ORFS in ${meta.id} against ${diamond_database}"
     label 'process_high'
     // Old diamond manual suggested *NOT* running in parallel... so we are setting maxForks to 1 here.
-    // TODO: There appears to be features for multiprocessing availabe now
+    // TODO: There appears to be features for multiprocessing available now
     // See: https://github.com/bbuchfink/diamond/wiki/6.-Distributed-computing
     maxForks 1
     publishDir "${params.interim_dir_internal}",

nextflow.config

@@ -128,34 +128,10 @@ try {
 }
 
 
-
-profiles {
-
-  standard {
-    // https://www.nextflow.io/docs/latest/executor.html#local
-    // simple profile that runs all processess locally
-
-    process.executor = "local"
-  }
-
-  slurm {
-    // https://www.nextflow.io/docs/latest/executor.html#slurm
-    // simple profile for running jobs on slurm
-
-    process.executor = "slurm"
-
-    // queue is the slurm partition to use.
-    // Set SLURM partition with queue directive.
-    process.queue = "queue"
-
-  }
-
-}
-
-
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     standard {
+        process.executer       = "local"
         docker.enabled         = true
         docker.userEmulation   = true
         singularity.enabled    = false
@@ -164,12 +140,18 @@ profiles {
         charliecloud.enabled   = false
     }
     slurm {
+    	process.executer       = "slurm"
+	// NOTE: You can determine your slurm partition (e.g. process.queue) with the `sinfo` command
+    	process.queue          = "queue"
         docker.enabled         = true
         docker.userEmulation   = true
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false
         charliecloud.enabled   = false
+        executor {
+            queueSize = 8
+        }
     }
     conda {
         params.enable_conda    = true