Adding Kraken to Krona conversion to blastoff.wdl #544
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| @@ -414,3 +414,13 @@ workflows: | |||
| primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz_general.wdl | |||
| testParameterFiles: | |||
| - /empty.json | |||
| - name: blastoff | |||
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Could you insert these added blocks above, so they're in alphabetical order with the other task names?
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| version 1.0 | |||
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| task trim_rmdup_subsamp { | |||
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Thanks for exposing assembly.py trim_rmdup_subsamp in a WDL task. Since the functionality isn't metablast-specific, could you move the task to tasks_read_utils.wdl? (and then change the location it's imported from in the workflows using it)
| assembly.py trim_rmdup_subsamp \ | ||
| "~{inBam}" \ | ||
| "~{clipDb}" \ | ||
| "$(pwd)/outbam.bam" \ |
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Could you expose the output bam among outputs of this task, so this task can be used independently for applications expecting bam-format?
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| #samtools [OutBam -> FASTA] | ||
| #-f 4 (f = include only) (4 = unmapped reads) https://broadinstitute.github.io/picard/explain-flags.html | ||
| samtools fasta "$(pwd)/outbam.bam" > "~{bam_basename}.fasta" |
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Maybe wrap the fasta output in a WDL conditional so it is only produced if a task input (emit_fasta, say) is set to true? (the task output would then need to have an optional File? type, since it may or may not exist)
This fasta has the potential to be quite large. Consider compressing it (with xz) here, and then decompress it in the task consuming it (iff it is compressed).
| version 1.0 | ||
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| task trim_rmdup_subsamp { | ||
| meta { |
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I thought we may want to mark this task as volatile: true, but it looks like the samtools-based downsampling in viral-core uses a constant seed, so it should be deterministic and we don't need to mark it as volatile.
| echo "--END STAGE 2" | ||
| echo "---START STAGE 3" | ||
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| #Stage 3 |
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A lot is going on in this stage. Can inline comments be added to walk through what's happening?
(and maybe also split up the long lines across multiple lines)
| } | ||
| parameter_meta { | ||
| krona_taxonomy_tab: { | ||
| description: "Krona taxonomy database containing a single file: 'taxonomy.tab' (exact name), or possibly just a compressed 'taxonomy.tab" |
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It would likely help users if the description says something about how to create or where to obtain a taxonomy.tab file (ex. "[...] as created by ktUpdateTaxonomy")
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| version 1.0 | |||
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| import "../tasks/tasks_megablast.wdl" as tools | |||
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Maybe change the input alias to something more descriptive like metablast rather than tools (& change usage below to match)
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| version 1.0 | |||
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| import "../tasks/tasks_megablast.wdl" as tools | |||
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Same comment as above about renaming the import alias to as megablast
| allowNestedInputs: true | ||
| } | ||
| input { | ||
| File inFasta |
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To be consistent, underscores rather than camel-case?
Kraken to Krona Conversion: Utilizes the krona command to convert Kraken output into Krona HTML visualizations, which allows for dynamic visualization of blastoff Kraken outputs.