Commit e3134618 authored by Thomas Van Parys's avatar Thomas Van Parys
Browse files

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

parent ab40bcb3
...@@ -96,6 +96,7 @@ assert params.name =~ /[a-zA-Z0-9_]+/ ...@@ -96,6 +96,7 @@ assert params.name =~ /[a-zA-Z0-9_]+/
//Input path must be absolute //Input path must be absolute
absInputPath = Paths.get(params.input).toAbsolutePath() absInputPath = Paths.get(params.input).toAbsolutePath()
// Parse species.txt // Parse species.txt
// Type: 'new', 'background', 'outgroup' // Type: 'new', 'background', 'outgroup'
Channel Channel
...@@ -353,7 +354,9 @@ process allVsAllProteomes { ...@@ -353,7 +354,9 @@ process allVsAllProteomes {
cpus 0 cpus 0
maxForks 300 maxForks 300
tag "$hitsName" tag "$hitsName"
publishDir "${params.output}/proteome_blast_all_vs_all", mode: 'copy' publishDir "${params.output}/proteome_blast_all_vs_all", mode: 'copy'
storeDir "${params.storage}/proteome_blast_all_vs_all"
input: input:
set file(fasta), database, databaseName, hitsName, speciesName, databaseSpeciesName from allVsAllInput set file(fasta), database, databaseName, hitsName, speciesName, databaseSpeciesName from allVsAllInput
...@@ -453,6 +456,8 @@ process ips { ...@@ -453,6 +456,8 @@ process ips {
module 'iprscan' // known stable iprscan/x86_64/5.22-61 . TODO old comment: the newer version crashed with stack trace due to a dependency problem (may have been fixed by now) module 'iprscan' // known stable iprscan/x86_64/5.22-61 . TODO old comment: the newer version crashed with stack trace due to a dependency problem (may have been fixed by now)
// this version is stable, newer versions caused all sorts of errors. TODO old comment: the newer version crashed with stack trace due to a dependency problem (may have been fixed by now) // this version is stable, newer versions caused all sorts of errors. TODO old comment: the newer version crashed with stack trace due to a dependency problem (may have been fixed by now)
publishDir "${params.output}/interproscan", mode: 'copy' publishDir "${params.output}/interproscan", mode: 'copy'
storeDir "${params.storage}/interproscan"
tag "$species" tag "$species"
cpus 8 cpus 8
memory '30 GB' memory '30 GB'
......
...@@ -67,6 +67,16 @@ params.venv_name = 'venv' ...@@ -67,6 +67,16 @@ params.venv_name = 'venv'
params.venv_home = '' 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 // Executor and per-process configuration
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment