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Update centrifuge/kreport
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parent
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commit
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3 changed files with 5 additions and 5 deletions
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@ -8,7 +8,7 @@ process CENTRIFUGE_KREPORT {
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'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
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input:
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tuple val(meta), path(results)
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tuple val(meta), path(report)
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path db
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output:
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@ -23,7 +23,7 @@ process CENTRIFUGE_KREPORT {
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
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centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt
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centrifuge-kreport -x \$db_name ${report} > ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -15,9 +15,9 @@ input:
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- results:
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- report:
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type: file
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description: File containing the centrifuge classification results
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description: File containing the centrifuge classification report
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pattern: "*.{txt}"
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output:
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@ -148,7 +148,7 @@ workflow PROFILING {
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}
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CENTRIFUGE_CENTRIFUGE ( ch_input_for_centrifuge.reads, ch_input_for_centrifuge.db, params.centrifuge_save_reads, params.centrifuge_save_reads, params.centrifuge_save_reads )
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CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.results, ch_input_for_centrifuge.db)
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CENTRIFUGE_KREPORT (CENTRIFUGE_CENTRIFUGE.out.report, ch_input_for_centrifuge.db)
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ch_versions = ch_versions.mix( CENTRIFUGE_CENTRIFUGE.out.versions.first() )
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ch_raw_classifications = ch_raw_classifications.mix( CENTRIFUGE_CENTRIFUGE.out.results )
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ch_raw_profiles = ch_raw_profiles.mix( CENTRIFUGE_KREPORT.out.kreport )
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