diff --git a/CHANGELOG.md b/CHANGELOG.md index ce42941e8c959e5c9af1f4b8b0d4f6478787183f..b11e42239411e49f47851e71781e97f52ddd78d5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ that users understand how the changes affect the new version. version 5.0.0-dev --------------------------- ++ Centrifuge: Remove metrics file from classification (which causes the + summary report to be empty). https://github.com/DaehwanKimLab/centrifuge/issues/83 + Add NanoPlot and NanoQC tasks. + Centrifuge: Add `timeMinutes` to `Classify` task and remove unnecessary downloading tasks (alternative is refseqtools). diff --git a/centrifuge.wdl b/centrifuge.wdl index bc2ea462df88b17a8d0065c9586a06978c3e0ca8..1e7a0b4566c1b782877ee37689a7a49045ea7fad 100644 --- a/centrifuge.wdl +++ b/centrifuge.wdl @@ -128,7 +128,6 @@ task Classify { ~{inputFormatOptions[inputFormat]} \ ~{true="--phred64" false="--phred33" phred64} \ --min-hitlen ~{minHitLength} \ - ~{"--met-file " + outputPrefix + "_alignment_metrics.tsv"} \ --threads ~{threads} \ ~{"--trim5 " + trim5} \ ~{"--trim3 " + trim3} \ @@ -143,7 +142,6 @@ task Classify { >>> output { - File metrics = outputPrefix + "_alignment_metrics.tsv" File classification = outputPrefix + "_classification.tsv" File report = outputPrefix + "_output_report.tsv" } @@ -175,7 +173,6 @@ task Classify { dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"} # outputs - metrics: {description: "File with centrifuge metrics."} classification: {description: "File with the classification results."} report: {description: "File with a classification summary."} }