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Added error free BAMs, optimized read processing and functions #35

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merged 59 commits into from
Nov 1, 2024

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farchaab
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@farchaab farchaab commented Oct 29, 2024

Summary

PR to add error free BAMS, remove redundant rules and simplify functions

Features

Changes

  • 65d0e9a Use xargs + cat to concatenate all fasta per sample
  • 3d3ee46 Only print three first fastqs per sample in cat_fastqs message
  • 24928f5 Added samtools container and env
  • 8c61950 Bumped assembly_finder's version
  • 4db4d03 Removed redundant cat rules
  • 6eda049 4fc53f4 Removed unused benchmarks and logs
  • 023de5b Improved functions syntax

Fixes

@farchaab farchaab marked this pull request as ready for review October 30, 2024 16:08
@farchaab farchaab changed the title Optimized read processing and functions Added error free BAMs, optimized read processing and functions Nov 1, 2024
@farchaab farchaab merged commit 6dd8f2d into main Nov 1, 2024
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@farchaab farchaab deleted the readproc branch November 1, 2024 14:31
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Error-free reads? CIGAR and query sequence are of different length with art_illumina
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