Code

Reorganize the results directory#67

Code

Merged

matthuska merged 26 commits intoMarieLataretu/issue55rki-mf1/clean:MarieLataretu/issue55from feature/reorganize-resultsrki-mf1/clean:feature/reorganize-resultsCopy head branch name to clipboardDec 14, 2023

+401-325

Commits

Commits on Nov 15, 2023

• Disable all publishDir directives. Add back the publishing of 'keep' output for now, to new dir with new name.

  matthuska

  committed
  fb759f5

Commits on Nov 16, 2023

• Place fastq files that map to 'keep' genome and to the host/control/own/rrna 'remove' genomes in appropriate intermediate folders

  matthuska

  committed
  df2497e

• Re-publish multiqc report to the qc/ directory (by default)

  matthuska

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  f739f8b

• Only publish sorted.bam{,.bai} intermediate bam files

  matthuska

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  b2ec355

• Publish idxstats and flagstats so they are next to their bam files

  matthuska

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  d91f94f

Commits on Nov 17, 2023

• Handle --strict_dcs and --min_clip output in results dir

  matthuska

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  82b60c0

• First steps towards making illumina/bbduk results dir look right

  matthuska

  committed
  fc1318b

Commits on Nov 19, 2023

• Add bed_samtools container bump minimap2 container (from main)

  matthuska

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  f03c8a5

Commits on Nov 21, 2023

• --keep is now working with bbduk. results/ is properly populated.

  matthuska

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  619c205

• Add seqkit conda environment file

  matthuska

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  4611647

• Output fasta when input is fasta

  Show description for e5e5659
  matthuska

  committed
  e5e5659

Commits on Nov 22, 2023

• Add --no_intermediate argument to skip publishing intermediate files to results/

  matthuska

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  753f97c

• Add singularity/ dir to .gitignore

  matthuska

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  bb499ac

• Tweak filter_fastq_by_name to work properly, avoid reading and writing to the same file in a pipe

  matthuska

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  14840fb

• Replace scary zcat/paste/grep/tr with seqkit grep

  matthuska

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  bb074a7

• Add clarifying comments to the filter_fastq_by_name process

  matthuska

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  40276ea

• Remove overwrite: false from publishDir directives

  matthuska

  committed
  dc59d28

Commits on Dec 10, 2023

• fix stub touch

  Show description for 39bd52e
  MarieLataretu

  committed
  39bd52e

• added seqkit to citations

  MarieLataretu

  committed
  d29a5ef

• Add -keep to help mssg. Reformated --help a bit. Removed old profiles for ARA and EBI.

  

  martin

  authored and

  martin

  committed
  d2ae118

• adjusted the README a bit

  

  martin

  authored and

  martin

  committed
  95ce2ee

• change sed command for --keep and add empty BED channel for phix control

  

  martin

  authored and

  martin

  committed
  975e05a

Commits on Dec 11, 2023

• Publish host genome and index for loading into IGV. Skipped if intermediate files are skipped.

  matthuska

  committed
  814e37b

• Switch to seqkit for check_own and concat_contamination

  matthuska

  committed
  5d87ac4

• bump seqkit container

  

  martin

  authored and

  martin

  committed
  4228c4b

Commits on Dec 13, 2023

• Update fastq_from_bam to publish illumina data properly. Regexes are geting crazy, need to rethink this.

  matthuska

  committed
  26bd1d0