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Add missing $prefix definition for MALT_RUN (#1373)

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* fix: remove left-over unnecessary code

* Add forgotten prefix for the log

* Update meta.yml

* Update tests

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
This commit is contained in:
James A. Fellows Yates 2022-03-03 17:58:04 +01:00 committed by GitHub
parent d8028dc1c3
commit 72b96f4e50
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 4 additions and 3 deletions
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3
modules/malt/run/main.nf
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@ -23,6 +23,7 @@ process MALT_RUN {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def avail_mem = 6 def avail_mem = 6
if (!task.memory) { if (!task.memory) {
log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
@ -39,7 +40,7 @@ process MALT_RUN {
$args \\ $args \\
--inFile ${fastqs.join(' ')} \\ --inFile ${fastqs.join(' ')} \\
-m $mode \\ -m $mode \\
--index $index/ |&tee malt-run.log --index $index/ |&tee ${prefix}-malt-run.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

2
modules/malt/run/meta.yml
View file

@ -52,7 +52,7 @@ output:
- log: - log:
type: file type: file
description: Log of verbose MALT stdout description: Log of verbose MALT stdout
pattern: "malt-run.log" pattern: "*-malt-run.log"
authors: authors:
- "@jfy133" - "@jfy133"

2
tests/modules/malt/run/test.yml
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@ -5,4 +5,4 @@
- malt/run - malt/run
files: files:
- path: output/malt/test_1.rma6 - path: output/malt/test_1.rma6
- path: output/malt/malt-run.log - path: output/malt/test-malt-run.log