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dahak-metagenomics / dahak

benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
https://dahak-metagenomics.github.io/dahak
BSD 3-Clause "New" or "Revised" License
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Read filtering Workflow: Not producing a MultiQC report #124

Open nalbright opened 6 years ago

nalbright commented 6 years ago

Expected behavior

Expect to find a multi QC report in outputs for read filtering workflow, but did not.

Actual behavior

No multi QC report is generated- (just a Fast QC report) It looks like it is specified in read filtering workflow (input config file), but does not generate a report.

Steps to reproduce the behavior

Ran assembly workflow as per documentation on Really quick Copy-and-Paste Quick Start

charlesreid1 commented 6 years ago

The MultiQC report is only part of the assembly workflow. There are only two places in the config file it should show up:

    "biocontainers" : {
        ...
        "multiqc" : {
            "use_local" : False,
            "quayurl" : "quay.io/biocontainers/multiqc",
            "version" : "1.4--py35_0"
        },
    "assembly" : {
        ...
        "assembly_patterns" : {

            ...

            "multiqc_pattern" : "{sample}.trim{qual}_{assembler}_multiqc/report.html",
        }
    },

In pointing this out, you did uncover another issue - there is no build rule defined in the assembly Snakefile to run this rule. I will make this change/add a build rule in a pull request.