millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 02:58:17 +00:00
Code Issues Releases Packages Activity

diminish memory demand (#1872)

Browse source 
* diminish memory demand

Kallisto was being told to ask for the same amount of memory as it was said for nextflow to limit.

So, when kallisto tried to use it, nextflow was killing it. Thus, diminishing it per 1 GB solved the issue.

* fix prettier

* removing TODOs
This commit is contained in:
Felipe Marques de Almeida 2022-07-12 15:53:02 +02:00 committed by GitHub
parent 589f39c39e
commit ec806cebf1
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
2 changed files with 3 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

3
modules/kallistobustools/count/main.nf
View file

@ -27,6 +27,7 @@ process KALLISTOBUSTOOLS_COUNT {
def prefix = task.ext.prefix ?: "${meta.id}"
def cdna = t1c ? "-c1 $t1c" : ''
def introns = t2c ? "-c2 $t2c" : ''
def memory = task.memory.toGiga() - 1
"""
kb \\
count \\
@ -39,7 +40,7 @@ process KALLISTOBUSTOOLS_COUNT {
$args \\
-o ${prefix}.count \\
${reads.join( " " )} \\
-m ${task.memory.toGiga()}G
-m ${memory}G
cat <<-END_VERSIONS > versions.yml
"${task.process}":

1
tests/modules/kallistobustools/count/test.yml
View file

@ -25,6 +25,7 @@
md5sum: b853330f160e06fc8af170a837384ef5
- path: output/kallistobustools/test.count/kb_info.json
- path: output/kallistobustools/test.count/matrix.ec
md5sum: 44eb94feb333b70cd3e55b6f4c0a43db
- path: output/kallistobustools/test.count/output.bus
md5sum: f5d8efa83f107826824292cbbdb4e37b
- path: output/kallistobustools/test.count/output.unfiltered.bus