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isugifNF / polishCLR

A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
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Remove old input code #57

Closed j23414 closed 1 year ago

j23414 commented 1 year ago

Input channels have been refactored to print out more descriptive messages for

  1. Errors on missing files:
[Missing File(s) Error] polishCLR requires a '--primary_assembly [primary fasta file]' to polish.
[Missing File(s) Error] polishCLR requires '--pacbio_reads [PacBio bam file]' for ArrowPolish steps.
[Missing File(s) Error] polishCLR requires '--illumina_reads [illumina_paired_end_{R1,R2}.fq]' for FreeBayes steps.
  1. Listing any provided files:
Primary Assembly: /Users/jchang3/Desktop/TEST_DATA/polishCLR/p_ctg.fasta 
Alternate Assembly: /Users/jchang3/Desktop/TEST_DATA/polishCLR/a_ctg_all.fasta 
Mitochondrial Assembly: /Users/jchang3/Desktop/TEST_DATA/polishCLR/mito.fasta 
PacBio Reads: /Users/jchang3/Desktop/TEST_DATA/polishCLR/test.1.filtered.bam
Illumina Reads: [testpolish, [/Users/jchang3/Desktop/TEST_DATA/polishCLR/testpolish_R1.fq, /Users/jchang3/Desktop/TEST_DATA/polishCLR/testpolish_R2.fq]]
  1. Suggestions for pipeline speedups
Creating the meryl database from the illumina reads. Passing in a precomputed meryl database via the '--meryldb [path/to/db]' flag may speed up QV checks in subsequent runs.

The old code was put into a comment block until we could test the new code.

Tests have completed so this commit is deleting the old code.