Added storage parameter. Used on ips and blast all vs all (#38)

main.nf

@@ -96,6 +96,7 @@ assert params.name =~ /[a-zA-Z0-9_]+/
 //Input path must be absolute
 absInputPath = Paths.get(params.input).toAbsolutePath()
 
+
 // Parse species.txt
 // Type: 'new', 'background', 'outgroup'
 Channel
@@ -353,7 +354,9 @@ process allVsAllProteomes {
     cpus 0
     maxForks 300
     tag "$hitsName"
+    
     publishDir "${params.output}/proteome_blast_all_vs_all", mode: 'copy'
+    storeDir "${params.storage}/proteome_blast_all_vs_all"
 
     input:
     set file(fasta), database, databaseName, hitsName, speciesName, databaseSpeciesName from allVsAllInput
@@ -453,6 +456,8 @@ process ips {
     module 'iprscan'  // known stable iprscan/x86_64/5.22-61 . TODO old comment: the newer version crashed with stack trace due to a dependency problem (may have been fixed by now)
     // this version is stable, newer versions caused all sorts of errors. TODO old comment: the newer version crashed with stack trace due to a dependency problem (may have been fixed by now)
     publishDir "${params.output}/interproscan", mode: 'copy'
+    storeDir "${params.storage}/interproscan"
+    
     tag "$species"
     cpus 8
     memory '30 GB'

nextflow.config.default

@@ -67,6 +67,16 @@ params.venv_name = 'venv'
 params.venv_home = ''
 
 
+/*
+ * Storage can be used to permanently store intermediate data that  
+ * can be re-used over different runs (eg. interpro scan)
+ * 
+ * It uses the Cedalion id's and will simply skip a process when the 
+ * exact output filename is found in storage.
+ *
+ * It will NOT check if input or process has changed!
+ */
+params.storage = 'storage'
 
 ///////////////////////////////////////////////////////////////////////////////
 // Executor and per-process configuration