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Update module: Use report insted of results for centrifuge/kreport (#1929)

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* Use report insted of results for kreport

* Update modules/centrifuge/kreport/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
This commit is contained in:
Sofia Stamouli 2022-07-27 14:24:06 +02:00 committed by GitHub
parent 31409f5e72
commit 734d0db607
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3 changed files with 12 additions and 14 deletions
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4
modules/centrifuge/kreport/main.nf
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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/centrifuge/kreport/meta.yml
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:

18
tests/modules/centrifuge/kreport/test.yml
View file

@ -1,21 +1,19 @@
- name: centrifuge kreport test_centrifuge_kreport_single_end - name: centrifuge kreport test_centrifuge_kreport_single_end
command: nextflow run tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_single_end -c tests/config/nextflow.config command: nextflow run ./tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_single_end -c ./tests/config/nextflow.config -c ./tests/modules/centrifuge/kreport/nextflow.config
tags: tags:
- centrifuge
- centrifuge/kreport - centrifuge/kreport
- centrifuge
files: files:
- path: output/centrifuge/test.report.txt
- path: output/centrifuge/test.results.txt
- path: output/centrifuge/test.txt - path: output/centrifuge/test.txt
md5sum: af1a51fe57eb6d428350ff4a4bf759d4
contains: ["unclassified"]
- path: output/centrifuge/versions.yml
- name: centrifuge kreport test_centrifuge_kreport_paired_end - name: centrifuge kreport test_centrifuge_kreport_paired_end
command: nextflow run tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/modules/centrifuge/kreport -entry test_centrifuge_kreport_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/centrifuge/kreport/nextflow.config
tags: tags:
- centrifuge
- centrifuge/kreport - centrifuge/kreport
- centrifuge
files: files:
- path: output/centrifuge/test.report.txt
- path: output/centrifuge/test.results.txt
- path: output/centrifuge/test.txt - path: output/centrifuge/test.txt
md5sum: af1a51fe57eb6d428350ff4a4bf759d4
contains: ["unclassified"]
- path: output/centrifuge/versions.yml