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Fix MALT multiqc report clash

This commit is contained in:
James Fellows Yates 2022-03-03 18:04:03 +01:00
parent 2c183ed2ed
commit e39c6a8ccb
4 changed files with 6 additions and 4 deletions

View file

@ -19,7 +19,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"malt/run": {
"git_sha": "76cdd46f3f8a77fb5023fb5a39c4ab99925b8b56"
"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
},
"multiqc": {
"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"

View file

@ -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}":

View file

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

View file

@ -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()
)