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Re-structure pipeline

Open KateSakharova opened this issue 4 months ago • 0 comments

Restructured pipeline to nf-core view

  • created main.nf main entry
  • added virify.nf to workflows and simplified
  • all subworkflows wrapped into separate files
  • modules moved to local/name/main.nf
  • publishDir moved to modules.config
  • container specified in each module main.nf
  • moved help to separate module
  • moved warning to separate module
  • removed CWL (woohoo)
  • added samplesheet support
  • removed --list option (replaced with samplesheet)

Now virify supports samplesheet (fq1 and fq2 are optional) id,assembly,fq1,fq2

For assembly as input: If you have assembly as input you can use old argument --fasta - that will run pipieline for 1 assembly. If you have more than 1 assembly - use samplesheet.

For raw_reads as input: You need to use ONLY samplesheet (even for 1 run). I replaced --illumina option with --assemble (boolean). User should specify that flag to force assembly process (that flag will help user to understand what he is doing). Hopefully, nobody uses it because it is experimental feature.

KateSakharova avatar Oct 01 '24 12:10 KateSakharova