mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 22:03:09 +00:00
Fix MALT multiqc report clash
This commit is contained in:
parent
2c183ed2ed
commit
e39c6a8ccb
4 changed files with 6 additions and 4 deletions
|
@ -19,7 +19,7 @@
|
|||
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
|
||||
},
|
||||
"malt/run": {
|
||||
"git_sha": "76cdd46f3f8a77fb5023fb5a39c4ab99925b8b56"
|
||||
"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
|
||||
},
|
||||
"multiqc": {
|
||||
"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
|
||||
|
|
3
modules/nf-core/modules/malt/run/main.nf
generated
3
modules/nf-core/modules/malt/run/main.nf
generated
|
@ -23,6 +23,7 @@ process MALT_RUN {
|
|||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def avail_mem = 6
|
||||
if (!task.memory) {
|
||||
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 \\
|
||||
--inFile ${fastqs.join(' ')} \\
|
||||
-m $mode \\
|
||||
--index $index/ |&tee malt-run.log
|
||||
--index $index/ |&tee ${prefix}-malt-run.log
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
2
modules/nf-core/modules/malt/run/meta.yml
generated
2
modules/nf-core/modules/malt/run/meta.yml
generated
|
@ -52,7 +52,7 @@ output:
|
|||
- log:
|
||||
type: file
|
||||
description: Log of verbose MALT stdout
|
||||
pattern: "malt-run.log"
|
||||
pattern: "*-malt-run.log"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
|
|
|
@ -203,7 +203,8 @@ workflow TAXPROFILER {
|
|||
ch_versions = ch_versions.mix(MALT_RUN.out.versions.first())
|
||||
}
|
||||
|
||||
|
||||
// TODO MALT results overwriting per database?
|
||||
// TODO Versions for Karken/MALT not report?
|
||||
MULTIQC (
|
||||
ch_multiqc_files.collect()
|
||||
)
|
||||
|
|
Loading…
Reference in a new issue