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Dev#81

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MarieLataretu merged 97 commits intomasterrki-mf1/clean:masterfrom devrki-mf1/clean:devCopy head branch name to clipboardJan 4, 2024

+816-340

Commits

Commits on May 17, 2022

• initial commit

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Commits on Jun 2, 2022

• check for bgzipped files

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  9dc3449

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• added pysam

  MarieLataretu

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• output also bams

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• split bam by name list

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Commits on Jun 10, 2022

• output index

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• added split fastq

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• split cleaned fastqs

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Commits on Jun 16, 2022

• split fastq by read names

  MarieLataretu

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  9f93ec4

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Commits on Jul 13, 2022

• mv keep to extra wf

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  68972e0

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• publish correct fastqs

  MarieLataretu

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  9c2b5ce

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• rm unused stuff

  MarieLataretu

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  74d8bbf

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• fixed bug for fasta input

  MarieLataretu

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  fa3113f

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• rm view

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Commits on Jul 15, 2022

• added publish mode param

  MarieLataretu

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  e1dbf5d

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• emit both bams

  MarieLataretu

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  77fa2cf

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• added typle for bam tuple

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• update publish

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• added type to bam

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• update publish

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  a0a5e99

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• renamed output

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  dea952b

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• added type

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  12e3ce4

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• update publish

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  06b817e

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• updated publish

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  c2e3359

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• added name

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  c0c1a20

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• works now for multiple sampes

  MarieLataretu

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Commits on Dec 2, 2022

• updated workflow figure

  MarieLataretu

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Commits on Sep 30, 2023

• Merge branch 'dev' into MarieLataretu/issue55

  MarieLataretu

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Commits on Oct 4, 2023

• Merge branch 'dev' into MarieLataretu/issue55

  MarieLataretu

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  86b3502

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Commits on Nov 2, 2023

• Fix some incorrect output names, conda envs, container for pigz

  matthuska

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Commits on Nov 8, 2023

• Merge pull request #64 from hoelzer/fix/issue55

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  MarieLataretu

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• Merge branch 'MarieLataretu/issue55' of github.com:hoelzer/clean into MarieLataretu/issue55

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• remove custom log file

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• Merge pull request #65 from hoelzer/change/rm_custom_log

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Commits on Nov 9, 2023

• Avoid zcat'ing *.gz when output file is also a .gz file. Can cause hangups and huge files. Use switch statement to simplify code.

  matthuska

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Commits on Nov 15, 2023

• Merge pull request #66 from hoelzer/fix/concat-carefully

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

  matthuska

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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

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

  matthuska

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

  matthuska

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  b2ec355

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

  matthuska

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Commits on Nov 17, 2023

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

  matthuska

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

  matthuska

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Commits on Nov 19, 2023

• Add bed_samtools container bump minimap2 container (from main)

  matthuska

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Commits on Nov 21, 2023

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

  matthuska

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• Add seqkit conda environment file

  matthuska

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• Output fasta when input is fasta

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Commits on Nov 22, 2023

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

  matthuska

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• Add singularity/ dir to .gitignore

  matthuska

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

  matthuska

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

  matthuska

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• Add clarifying comments to the filter_fastq_by_name process

  matthuska

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• Remove overwrite: false from publishDir directives

  matthuska

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Commits on Dec 10, 2023

• fix stub touch

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  MarieLataretu

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• added seqkit to citations

  MarieLataretu

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

  

  martin

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  martin

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• adjusted the README a bit

  

  martin

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

  

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  975e05a

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Commits on Dec 11, 2023

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

  matthuska

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• Switch to seqkit for check_own and concat_contamination

  matthuska

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  5d87ac4

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• bump seqkit container

  

  martin

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Commits on Dec 13, 2023

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

  matthuska

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Commits on Dec 14, 2023

• Merge pull request #67 from hoelzer/feature/reorganize-results

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• Merge branch 'dev' into MarieLataretu/issue55

  MarieLataretu

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  dea8a3e

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• linked to correct workflow figure

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  f50812e

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• Merge pull request #70 from hoelzer/MarieLataretu/issue55

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Commits on Dec 15, 2023

• added nf-tests

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Commits on Dec 16, 2023

• update the repo location

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• Merge pull request #71 from rki-mf1/fix/update-repo-home

  MarieLataretu

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  65b836c

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• added on trigger

  MarieLataretu

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  e2b381a

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• fix test config location

  MarieLataretu

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  88244b9

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• enable singularity tests

  MarieLataretu

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  f5361f4

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• disable singularity tests due to Failed to pull singularity image errors

  MarieLataretu

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  6a0ad65

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• bump action/cache v3

  MarieLataretu

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  c899aca

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• enable conda tests

  MarieLataretu

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  528417d

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• adde paired-end publishing with keep

  MarieLataretu

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  be9620d

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• extended results example in readme

  MarieLataretu

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  17745d6

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• add acknow

  

  martin

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  bb9e91b

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• typo

  

  martin

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  ba5815a

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• fix copy paste error

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  MarieLataretu

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• Merge branch 'fix/results-orga-keep' of github.com:hoelzer/clean into fix/results-orga-keep

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Commits on Dec 18, 2023

• Merge pull request #72 from rki-mf1/fix/results-orga-keep

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Commits on Dec 20, 2023

• Bump setup-miniconda to v3, to support libmamba solver for conda. Set solver explicitly.

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Commits on Jan 3, 2024

• Merge pull request #73 from rki-mf1/feature/bump-conda-action

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  MarieLataretu

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• fix stub

  MarieLataretu

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  645b7f3

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• publish (un)mapped_merged with keep

  MarieLataretu

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  bfdc856

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• Merge pull request #75 from rki-mf1/fix/reorganize-results

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• Change zcat comands to read file from stdin

  matthuska

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• Merge pull request #77 from rki-mf1/fix/zcat-mac

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  matthuska

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• Run dryrun action on PR against main or dev, and pushes directly to main

  matthuska

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• Add python-version to matrix (fixed to 3.9 for now), and include nextflow version in job name

  matthuska

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• Merge pull request #78 from rki-mf1/fix/actions-on-dev-pr

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• create an uncompressed index instead of a compressed one

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• Merge pull request #79 from rki-mf1/MarieLataretu/issue74

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• updated changelog

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Commits on Jan 4, 2024

• updated changelog

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• changed main to master

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