dsl2 port #199
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dsl2 port #199
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* fastqc * picard/markduplicates * preseq/lcextrap * samtools/flagstat * samtools/index * samtools/stats * samtools/sort * trimgalore * multiqc
* bismark/genome_preparation * bismark/align * bismark/deduplicate * bismark/extract * bismark/report * bismark/summary TODO: write tests and add to nf-core/modules
* bwameth/align * bwameth/index TODO: write tests and add to nf-core/modules
* methyldackel/extract * methyldackel/mbias TODO: write tests and add to nf-core modules
TODO: write tests and add to nf-core/modules
TODO: write tests and add to nf-core/modules
this is inspired by the functionality in nf-core/nanoseq and nf-core/rnaseq The idea is to require a samplesheet to run the pipeline, which will allow for single/paired end auto-detection and mapping samples against different reference genomes. addresses #181
TODO: needs change in nf-core/test-datasets
baseDir is deprecated
* fastqc * picard/markduplicates * preseq/lcextrap * samtools/flagstat * samtools/index * samtools/stats * samtools/sort * trimgalore * multiqc
* bismark/genome_preparation * bismark/align * bismark/deduplicate * bismark/extract * bismark/report * bismark/summary TODO: write tests and add to nf-core/modules
* bwameth/align * bwameth/index TODO: write tests and add to nf-core/modules
* methyldackel/extract * methyldackel/mbias TODO: write tests and add to nf-core modules
TODO: write tests and add to nf-core/modules
TODO: write tests and add to nf-core/modules
this is inspired by the functionality in nf-core/nanoseq and nf-core/rnaseq The idea is to require a samplesheet to run the pipeline, which will allow for single/paired end auto-detection and mapping samples against different reference genomes. addresses #181
TODO: needs change in nf-core/test-datasets
Try to avoid the warning about having duplicate processes
Final (?!) updates to `dsl2` before merge
Update methylkit/extract module.
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Let's do it! |
ewels
approved these changes
Nov 3, 2022
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Continuation of #182 (now from a dedicated branch)
The pipeline now requires a sample sheet to be passed to the pipeline with
--input:See an example here
The
genomecolumn is optional,--genomecontinues to work as wellKnown issues:
workflow summary shows NAs-> (fixed by @ewels in Rewrite the schema summary log #206)MultiQCreport is missing some data-profile test_fullneeds asamplesheet.csv