diff --git a/modules/centrifuge/kreport/main.nf b/modules/centrifuge/kreport/main.nf index 124cbdba..381ddd6c 100644 --- a/modules/centrifuge/kreport/main.nf +++ b/modules/centrifuge/kreport/main.nf @@ -8,7 +8,7 @@ process CENTRIFUGE_KREPORT { 'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }" input: - tuple val(meta), path(results) + tuple val(meta), path(report) path db output: @@ -23,7 +23,7 @@ process CENTRIFUGE_KREPORT { def prefix = task.ext.prefix ?: "${meta.id}" """ 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} > ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/centrifuge/kreport/meta.yml b/modules/centrifuge/kreport/meta.yml index fbcae24f..822a280e 100644 --- a/modules/centrifuge/kreport/meta.yml +++ b/modules/centrifuge/kreport/meta.yml @@ -15,9 +15,9 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - results: + - report: type: file - description: File containing the centrifuge classification results + description: File containing the centrifuge classification report pattern: "*.{txt}" output: diff --git a/tests/modules/centrifuge/kreport/test.yml b/tests/modules/centrifuge/kreport/test.yml index 167cb0dc..ab614c53 100644 --- a/tests/modules/centrifuge/kreport/test.yml +++ b/tests/modules/centrifuge/kreport/test.yml @@ -1,21 +1,19 @@ - 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: - - centrifuge - centrifuge/kreport + - centrifuge files: + - path: output/centrifuge/test.report.txt + - path: output/centrifuge/test.results.txt - path: output/centrifuge/test.txt - md5sum: af1a51fe57eb6d428350ff4a4bf759d4 - contains: ["unclassified"] - - path: output/centrifuge/versions.yml - 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: - - centrifuge - centrifuge/kreport + - centrifuge files: + - path: output/centrifuge/test.report.txt + - path: output/centrifuge/test.results.txt - path: output/centrifuge/test.txt - md5sum: af1a51fe57eb6d428350ff4a4bf759d4 - contains: ["unclassified"] - - path: output/centrifuge/versions.yml