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Update centrifuge/kreport

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This commit is contained in:
sofstam 2022-07-27 14:42:35 +02:00
parent fdd9a3bc4d
commit cecbb41f88
3 changed files with 5 additions and 5 deletions
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4
modules/nf-core/modules/centrifuge/kreport/main.nf generated
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@ -8,7 +8,7 @@ process CENTRIFUGE_KREPORT {
'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }" 'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
input: input:
tuple val(meta), path(results) tuple val(meta), path(report)
path db path db
output: output:
@ -23,7 +23,7 @@ process CENTRIFUGE_KREPORT {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'` db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

4
modules/nf-core/modules/centrifuge/kreport/meta.yml generated
View file

@ -15,9 +15,9 @@ input:
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- results: - report:
type: file type: file
description: File containing the centrifuge classification results description: File containing the centrifuge classification report
pattern: "*.{txt}" pattern: "*.{txt}"
output: output:

2
subworkflows/local/profiling.nf
View file

@ -148,7 +148,7 @@ workflow PROFILING {
} }
CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads ) CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db) CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.report, ch_input_for_centrifuge.db)
ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() ) ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results ) ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport ) ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )