Code

Pipes#91

Code

Merged

muffato merged 16 commits intodevsanger-tol/readmapping:devfrom pipessanger-tol/readmapping:pipesCopy head branch name to clipboardJun 11, 2024

+442-542

Commits

Commits on Jan 25, 2024

• Created a local module to convert to Fasta without intermediate files

  muffato

  committed
  e370b8c

• Simplified the topology of the pipeline by instantiating the CONVERT_STATS sub-workflow just once

  muffato

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  04c160d

• Rolled out the minimap2 -I setting to all data types

  muffato

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  6565f93

• Combined two consecutive samtools steps to save some space

  muffato

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  b3cb5d8

• Sort the BAM file directly with bwamem2 to save some disk space

  muffato

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  3d7a700

• Merged the markdup_stats sub-workflow into align_illumina

  muffato

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  0e21eaf

• Mistletoe (96Gbp, 2.4 M reads) takes 210 GB RAM and slightly over 2 hours

  muffato

  committed
  15ad23d

Commits on Feb 2, 2024

• Updated the minimap2/align module to the latest nf-core version

  Show description for 3d71db7
  muffato

  committed
  3d71db7

Commits on Feb 6, 2024

• Updated the crumble module to keep it closer to the original

  muffato

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  7a9671c

• We don't need the suspicious regions

  muffato

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  cfb7977

• Also compress the Illumina files with crumble, and don't compress the pre-cumble BAMs

  muffato

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  20536ea

• Not needed because crumble now outputs BAM

  muffato

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  7cbb416

Commits on Feb 9, 2024

• Sort the BAM files before merging to make the output reproducible

  muffato

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  c76d9a9

Commits on Jun 5, 2024

• Memory settings for ALIGN_ONT:MINIMAP2_ALIGN

  muffato

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  7ba557c

Commits on Jun 6, 2024

• Bumped the version and updated the changelog

  muffato

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  92b4744

• The patch was missing

  muffato

  committed
  8299694