Merge pull request #19 from sanger-tol/longranger_lsf

Updated config for running longranger with and without LSF
sanger-tol · Sep 11, 2023 · c6ce6fb · c6ce6fb
2 parents 3768dec + dfafb26
commit c6ce6fb
Show file tree

Hide file tree

Showing 3 changed files with 34 additions and 8 deletions.
diff --git a/conf/longranger_lsf_sanger.config b/conf/longranger_lsf_sanger.config
@@ -0,0 +1,17 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running longranger on LSF at the Sanger
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process {
+    withName: LONGRANGER_ALIGN {
+        // Same arguments as in conf/modules.config but with the LSF job mode
+        ext.args = "--disable-ui --nopreflight --jobmode=lsf"
+    }
+}
+
+// Make the LSF configuration available to the container / longranger
+singularity.envWhitelist = "LSF_BINDIR,LSF_SERVERDIR,LSF_LIBDIR,LSF_ENVDIR"
+singularity.runOptions   = "-B ${projectDir}/assets/martian.lsf.template:/opt/longranger-2.2.2/martian-cs/2.3.2/jobmanagers/lsf.template -B /software -B /etc/lsf.conf --env APPEND_PATH=$LSF_BINDIR:$LSF_SERVERDIR:/software/singularity-v3.9.0/bin"
+
diff --git a/conf/modules.config b/conf/modules.config
@@ -367,8 +367,9 @@ process {
     // Set up of the polishing pipeline
 
     withName: LONGRANGER_MKREF {
-        envWhitelist = "LSF_BINDIR,LSF_SERVERDIR,LSF_LIBDIR,LSF_ENVDIR"
-        runOptions = "-B ${projectDir}/martian.lsf.template:/opt/longranger-2.2.2/martian-cs/2.3.2/jobmanagers/lsf.template -B /software -B /etc/lsf.conf --env APPEND_PATH=$LSF_BINDIR:$LSF_SERVERDIR:/software/singularity-v3.9.0/bin"
+        if(System.getenv('GITHUB_ACTION') != null ) {
+            container = "ghcr.io/sanger-tol/longranger:2.2.2-c3"
+        }
         publishDir = [
             path: { "${params.outdir}/${meta.id}.${params.hifiasm}/polishing" },
             mode: params.publish_dir_mode,
@@ -377,14 +378,11 @@ process {
     }
 
     withName: LONGRANGER_ALIGN {
+        // Keep in sync with `longranger_lsf_sanger.config`
         ext.args = "--disable-ui --nopreflight"
         if(System.getenv('GITHUB_ACTION') != null ) {
             container = "ghcr.io/sanger-tol/longranger:2.2.2-c3"
         }
-        else {
-            envWhitelist = "LSF_BINDIR,LSF_SERVERDIR,LSF_LIBDIR,LSF_ENVDIR"
-            runOptions = "-B ${projectDir}/martian.lsf.template:/opt/longranger-2.2.2/martian-cs/2.3.2/jobmanagers/lsf.template -B /software -B /etc/lsf.conf --env APPEND_PATH=$LSF_BINDIR:$LSF_SERVERDIR:/software/singularity-v3.9.0/bin"
-        }
         publishDir = [
             path: { "${params.outdir}/${meta.id}.${params.hifiasm}/polishing" },
             mode: params.publish_dir_mode,
@@ -677,3 +675,16 @@ process {
     //End of Set up of assmebly stats subworkflow
 
 }
+
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Extra profiles defined to override some of the above parameters
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Importantly, these profiles *cannot* be defined in the main `nextflow.config`,
+    otherwise they would be loaded _before_ this `conf/modules.config`.
+----------------------------------------------------------------------------------------
+*/
+profiles {
+    longranger_lsf_sanger { includeConfig 'longranger_lsf_sanger.config' }
+}
diff --git a/nextflow.config b/nextflow.config
@@ -127,8 +127,6 @@ profiles {
         shifter.enabled        = false
         apptainer.enabled      = false
         charliecloud.enabled   = false
-        singularity.envWhitelist = "LSF_BINDIR,LSF_SERVERDIR,LSF_LIBDIR,LSF_ENVDIR"
-        singularity.runOptions = "-B ${projectDir}/assets/martian.lsf.template:/opt/longranger-2.2.2/martian-cs/2.3.2/jobmanagers/lsf.template -B /software -B /etc/lsf.conf --env APPEND_PATH=$LSF_BINDIR:$LSF_SERVERDIR:/software/singularity-v3.9.0/bin"
     }
     podman {
         podman.enabled         = true