Code

Dev#54

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Merged

MarieLataretu merged 119 commits intomasterrki-mf1/clean:masterfrom devrki-mf1/clean:devCopy head branch name to clipboardSep 30, 2023

+809-638

Commits

Commits on Jun 24, 2021

• removed unused output

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  a06a086

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Commits on Jun 25, 2021

• test teloclip, rm code redundancy

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  eaffc5c

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• assembly

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Commits on Jun 29, 2021

• added custom soft-clip filter

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  2a8b433

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• added env

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  de98d8a

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• added the right env

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  30d0ab6

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Commits on Jul 1, 2021

• switch to https cloning

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  f0a08c5

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• added mem

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Commits on Jul 7, 2021

• other parameter

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  e5d7125

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• Merge branch 'MarieLataretu/issue23' of github.com:hoelzer/clean into MarieLataretu/issue23

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  1c9cbd1

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• https and ssh cloning

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  655cda1

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• cli param for minClip

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  7cc48cd

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• bam also for fasta

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Commits on Jul 14, 2021

• Merge branch 'master' into dev

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  d8a3df0

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Commits on Jul 21, 2021

• added fastq from bam

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  513a501

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• handle also paired-end reads

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  58f8d3c

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• Merge pull request #39 from hoelzer/MarieLataretu/issue23

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Commits on Jul 29, 2021

• reference index file incomplete

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Commits on Jul 30, 2021

• Merge pull request #41 from hoelzer/MarieLataretu/issue40

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Commits on Aug 10, 2021

• hotfix minimap2 fasta

  MarieLataretu

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  b3c5679

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Commits on Sep 10, 2021

• rename output,fix multiqc barplot,add ambig stats

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  committed
  6d65177

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• update also for illumina, rm foo xD

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  ee9c855

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• typo

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  a84efef

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• first commit

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  27d8ecd

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Commits on Sep 13, 2021

• fixes #42

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  d559162

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Commits on Sep 14, 2021

• Merge pull request #43 from hoelzer/MarieLataretu/issue42

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• added min_clip to help

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  92a4668

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• --min_clip, typo

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  303e8f8

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Commits on Sep 27, 2021

• fixed stats for fasta

  MarieLataretu

  committed
  a9cbdd0

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• idxstats for fasta

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  64cb857

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Commits on Oct 14, 2021

• hotfix and typos

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  committed
  c743f58

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Commits on Nov 25, 2021

• add --split-prefix to minimap2

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• problem when input files end with clean

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  ef4f78e

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• do concat_contamination only once

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• make contig names unique when con#44 fix

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Commits on Jan 27, 2022

• Merge pull request #48 from hoelzer/MarieLataretu/issue46

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• Merge branch 'dev' into MarieLataretu/issue45

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• Merge pull request #49 from hoelzer/MarieLataretu/issue45

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Commits on Jan 28, 2022

• Merge branch 'dev' into MarieLataretu/issue47

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• Merge pull request #50 from hoelzer/MarieLataretu/issue47

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Commits on Feb 2, 2022

• header renaming only if multiple fastas

  MarieLataretu

  committed
  0fc3376

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Commits on Feb 3, 2022

• added use mamba

  MarieLataretu

  committed
  21a3574

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• code style

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  899366a

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• code style

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  7c75b7e

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• use addParams

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  7deed84

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• use addParams

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  56dcfcd

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• addParams

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  9845b2a

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• filter true dcs

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  committed
  41fa17b

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• separate wf

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  1dadd2f

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• separate qc wf

  MarieLataretu

  committed
  b449e70

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• one minimap2 process

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  committed
  53e8cd0

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• first clean subworkflow

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  40193e2

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Commits on Feb 4, 2022

• separate contamination wf

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  committed
  1f01a28

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• added stubs, errors, name variable

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  c60d776

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• restruc write log

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  3bd653e

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Commits on Feb 5, 2022

• fix bug, fix whitespaces

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  committed
  dc39535

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• mv contig countig to countig process

  MarieLataretu

  committed
  ed006c1

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• fixed output, fixed naming

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  committed
  f486da7

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Commits on Feb 10, 2022

• allow only one input type

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  committed
  09976ea

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• filter true dcs

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  committed
  880e664

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• added -@

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  cd3de03

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• split bam, merge bam

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  84a2e5d

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Commits on Feb 18, 2022

• clean wf structure

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  committed
  18e6e5a

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Commits on Feb 25, 2022

• added vscode

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  committed
  a04e98d

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• simplified input params

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  committed
  997d505

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• documented input change

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  65e1c3c

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• added comments

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  d0103a1

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• rm name

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  4a2aef8

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• rm name

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  e59c952

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• added processes

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  committed
  0b8f7c7

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• fixed idxstats

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  54a3630

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• renamed mode

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  c24feea

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• correct spliting

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  ddf0fd1

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• renamed mode, extended stub

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  d8ac096

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• qc remasterd

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  c2ed4de

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• condensed sub wfs

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  53e88cd

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• extended wf

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  8873e44

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• updated params

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  76607b4

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• removed process

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  f0c7f56

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• updated processes

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  05682e1

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• updated minimap2

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  55ebe43

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• added name to stats file

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  9510811

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• added collect

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  c5a6339

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• fix empty handling

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  committed
  4ec2d86

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• fixed and updated

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  committed
  25d9286

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• fixed and updated merged bam

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  13233b5

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• bed file channel

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  eec7484

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• dcs filtering

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  cfebcfb

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• softclip filter

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  committed
  0645972

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• avoid overwriting at merging

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  committed
  6e42522

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• renamed softclip filter output

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  9f41256

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• added index for bams

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  5923cc9

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Commits on Mar 4, 2022

• moved unused processes

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  71eaf6a

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Commits on Mar 7, 2022

• added dcs_strict parameter

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  156fb3e

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Commits on Mar 17, 2022

• updated version

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Commits on May 5, 2022

• Merge branch 'master' into dev

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  ec31c2b

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• Merge branch 'master' into dev

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  b539ee1

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• updated readme

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  e68cb1d

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Commits on May 12, 2022

• added missing varable for eno

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Commits on May 17, 2022

• remmoved old stats line

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  95b5ab5

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Commits on Dec 9, 2022

• fixed typo

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  2aa6b81

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• fix fasta input

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  425b0bf

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• added conda profile

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Commits on Jan 13, 2023

• publish results in sample specific subdirs

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• publish idxstats

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Commits on Jan 17, 2023

• make naming more consistent

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• rename sorted bams

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Commits on May 29, 2023

• fix channels for host and own FASTA input

  

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• fix ownFastaChannel empty

  

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  d2ce97b

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• bump minimap2 and samtools version

  

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Commits on Jun 21, 2023

• Update nextflow.config

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• added citations

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Commits on Sep 29, 2023

• readme updates

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• added --cleanup_work_dir

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Commits on Sep 30, 2023

• directly compress and publish reads/fastas

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• make cleanup_work_dir a valid parameter

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  a19b0d9

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• Merge pull request #59 from hoelzer/feature_clean-work-dir

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• added changelog

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• minor text change

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