Cat fastq feature #179
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Cat fastq feature #179
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Has more useful parsing/validation methods, which would be relevant as this pipeline takes multiple possible data types (i.e. bams and/or fastqs).
…catenated in channel. Logic borrowed from nf-core rnaseq: https://github.com/nf-core/rnaseq/blob/b96a75361a4f1d49aa969a2b1c68e3e607de06e8/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf#L158-L174
meta.id is appended to front of list to facilitate joining by `.groupTuple()`, and is eventually dropped by `checkSamplesAfterGrouping` which returns `[meta, input_files]` as expected by rest of pipeline.
…lacing with tests in schema_input.json.
This PR is against the
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Apologies, should have worked off `dev` to begin with.
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Thanks @SpikyClip, I will have a look later today. 👍 |
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Changes
cat_fastqmodule which allows merging of resequenced fastq files before samples are processed downstream, fixes No cat_fastq? Sample with multiple run are not handled #148.nf-schemawas also added and samplesheet tests introduced (facilitated by the plugin's functionsamplesheetToList).test_fastq_cat), also included intest_full. Original test sample data was split withseqkitinto two parts.schema_input.jsonupdated to2020-12json standard.Potential Issues
nextflow_schema.jsonto2020-12, even when following the migration guide. For some reason doing so results in the error message:nextflow_schema.json, it just failsnf-core pipeline lint.PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).