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Recent Releases of clean

clean - v1.1.2

What's Changed

  • Update dev to latest main by @hoelzer in https://github.com/rki-mf1/clean/pull/116
  • add pacbio specific minimap2 parameter and input option by @hoelzer in https://github.com/rki-mf1/clean/pull/117
  • Dev by @hoelzer in https://github.com/rki-mf1/clean/pull/118

Full Changelog: https://github.com/rki-mf1/clean/compare/v1.1.1...v1.1.2

- Nextflow
Published by hoelzer over 1 year ago

clean - v1.1.1

What's Changed

  • Try to resolve intermittant conda-related CI failures by @matthuska in https://github.com/rki-mf1/clean/pull/112
  • Change check_own process to not include input files in output by @matthuska in https://github.com/rki-mf1/clean/pull/113

Full Changelog: https://github.com/rki-mf1/clean/compare/v1.1.0...v1.1.1

- Nextflow
Published by hoelzer over 1 year ago

clean - v1.1.0

What's Changed

  • Summary file for number and proportion of mapped and unmapped reads by @ayoraind in https://github.com/rki-mf1/clean/pull/106
  • Add bwa by @MarieLataretu in https://github.com/rki-mf1/clean/pull/103
  • Increase RAM by @hoelzer in https://github.com/rki-mf1/clean/pull/101
  • fix bbduk which has no bam channel for the new summary script by @hoelzer in https://github.com/rki-mf1/clean/pull/108
  • Dev by @hoelzer in https://github.com/rki-mf1/clean/pull/111

New Contributors

  • @ayoraind made their first contribution in https://github.com/rki-mf1/clean/pull/106

Full Changelog: https://github.com/rki-mf1/clean/compare/v1.0.3...v1.1.0

- Nextflow
Published by hoelzer over 1 year ago

clean - v1.0.3

What's Changed

  • Set default branch to 'main' instead of the Nextflow default 'master' by @matthuska in https://github.com/rki-mf1/clean/pull/92
  • Remove 'conda clean' from GitHub action to avoid random crashes by @matthuska in https://github.com/rki-mf1/clean/pull/96
  • Bump github action versions for node 16 -> 20 change by @matthuska in https://github.com/rki-mf1/clean/pull/94
  • Add T2T homo sapiens genome as additional auto-download option by @hoelzer in https://github.com/rki-mf1/clean/pull/99
  • Dev by @hoelzer in https://github.com/rki-mf1/clean/pull/100

Full Changelog: https://github.com/rki-mf1/clean/compare/v1.0.2...v1.0.3

- Nextflow
Published by hoelzer almost 2 years ago

clean - Version v1.0.2

What's Changed

  • Add --skip_qc to allow skipping fastqc/nanoplot/multiqc by @matthuska in https://github.com/rki-mf1/clean/pull/90

Full Changelog: https://github.com/rki-mf1/clean/compare/v1.0.1...v1.0.2

- Nextflow
Published by MarieLataretu about 2 years ago

clean - v1.0.1

What's Changed

  • add sc2 autodownload by @hoelzer in https://github.com/rki-mf1/clean/pull/87

Full Changelog: https://github.com/rki-mf1/clean/compare/v1.0.0...v1.0.1

- Nextflow
Published by hoelzer over 2 years ago

clean - v1.0.0

What's Changed

  • Marie lataretu/issue23 by @MarieLataretu in https://github.com/rki-mf1/clean/pull/39
  • reference index file incomplete by @MarieLataretu in https://github.com/rki-mf1/clean/pull/41
  • Marie lataretu/issue42 by @MarieLataretu in https://github.com/rki-mf1/clean/pull/43
  • problem when input files end with clean by @MarieLataretu in https://github.com/rki-mf1/clean/pull/48
  • add --split-prefix to minimap2 by @MarieLataretu in https://github.com/rki-mf1/clean/pull/49
  • Marie lataretu/issue47 by @MarieLataretu in https://github.com/rki-mf1/clean/pull/50
  • Updates for cloud run by @hoelzer in https://github.com/rki-mf1/clean/pull/51
  • check for newlines when concat fastas by @MarieLataretu in https://github.com/rki-mf1/clean/pull/53
  • Feature clean work dir by @MarieLataretu in https://github.com/rki-mf1/clean/pull/59
  • Dev by @MarieLataretu in https://github.com/rki-mf1/clean/pull/54
  • Dev by @MarieLataretu in https://github.com/rki-mf1/clean/pull/61
  • Add SARS-CoV-2 as an easy to use species by @matthuska in https://github.com/rki-mf1/clean/pull/63
  • Fixes a few issues in the ML/issue55 branch by @matthuska in https://github.com/rki-mf1/clean/pull/64
  • remove custom log file by @MarieLataretu in https://github.com/rki-mf1/clean/pull/65
  • Avoid zcat'ing *.gz when output file is also a .gz file. by @matthuska in https://github.com/rki-mf1/clean/pull/66
  • Add bed_samtools container by @matthuska in https://github.com/rki-mf1/clean/pull/69
  • Reorganize the results directory by @matthuska in https://github.com/rki-mf1/clean/pull/67
  • Marie lataretu/issue55 by @MarieLataretu in https://github.com/rki-mf1/clean/pull/70
  • Fix/update-repo-home by @MarieLataretu in https://github.com/rki-mf1/clean/pull/71
  • Fix/results-orga-keep by @MarieLataretu in https://github.com/rki-mf1/clean/pull/72
  • GitHub Action: Bump setup-miniconda to v3, to support libmamba solver for conda by @matthuska in https://github.com/rki-mf1/clean/pull/73
  • Fix/reorganize results by @MarieLataretu in https://github.com/rki-mf1/clean/pull/75
  • Fix zcat problems on mac by @matthuska in https://github.com/rki-mf1/clean/pull/77
  • Run dryrun action on PR against main or dev, and pushes directly to main by @matthuska in https://github.com/rki-mf1/clean/pull/78
  • create an uncompressed index instead of a compressed one by @MarieLataretu in https://github.com/rki-mf1/clean/pull/79
  • Dev by @MarieLataretu in https://github.com/rki-mf1/clean/pull/81

New Contributors

  • @matthuska made their first contribution in https://github.com/rki-mf1/clean/pull/63

Full Changelog: https://github.com/rki-mf1/clean/compare/v0.2.0...v1.0.0

- Nextflow
Published by MarieLataretu over 2 years ago

clean - v1.0.0-beta.2

What's Changed

  • Add SARS-CoV-2 as an easy-to-use species by @matthuska in https://github.com/hoelzer/clean/pull/63
  • added proxy information forwarding for Singularity usage (can cause problems on HPCs)

New Contributors

  • @matthuska made their first contribution in https://github.com/hoelzer/clean/pull/63

Full Changelog: https://github.com/hoelzer/clean/compare/v1.0.0-beta.1...v1.0.0-beta.2

- Nextflow
Published by hoelzer over 2 years ago

clean - v1.0.0-beta.1

What's Changed

  • changed minimap2 container by @MarieLataretu in https://github.com/hoelzer/clean/pull/61

Full Changelog: https://github.com/hoelzer/clean/compare/v1.0.0-beta...v1.0.0-beta.1

- Nextflow
Published by MarieLataretu over 2 years ago

clean - v1.0.0-beta

What's Changed

  • Marie lataretu/issue23 by @MarieLataretu in https://github.com/hoelzer/clean/pull/39
  • reference index file incomplete by @MarieLataretu in https://github.com/hoelzer/clean/pull/41
  • Marie lataretu/issue42 by @MarieLataretu in https://github.com/hoelzer/clean/pull/43
  • problem when input files end with clean by @MarieLataretu in https://github.com/hoelzer/clean/pull/48
  • add --split-prefix to minimap2 by @MarieLataretu in https://github.com/hoelzer/clean/pull/49
  • Marie lataretu/issue47 by @MarieLataretu in https://github.com/hoelzer/clean/pull/50
  • Updates for cloud run by @hoelzer in https://github.com/hoelzer/clean/pull/51
  • check for newlines when concat fastas by @MarieLataretu in https://github.com/hoelzer/clean/pull/53
  • Feature clean work dir by @MarieLataretu in https://github.com/hoelzer/clean/pull/59
  • Dev by @MarieLataretu in https://github.com/hoelzer/clean/pull/54

Full Changelog: https://github.com/hoelzer/clean/compare/v0.2.0...v1.0.0-beta

Usage changes

  • input parameter usage:
    • before: --[nano|illumina|illumina_single_end|fasta]
    • now: --input_type [nano|illumina|illumina_single_end|fasta] --input *.fastq

- Nextflow
Published by MarieLataretu over 2 years ago

clean - v0.2.0

  • removed needless renaming of read names

- Nextflow
Published by MarieLataretu almost 5 years ago

clean - v0.1.2

  • full DNA CS sequence (from Guppy)

- Nextflow
Published by MarieLataretu almost 5 years ago

clean -

  • fixed bug in list input mode

- Nextflow
Published by MarieLataretu almost 6 years ago

clean - Initial release

Clean your data (fasta files, Illumina reads or Nanopore (ONT) reads) against spike-in or custom sequences.

Supported species: - Homo sapiens - Mus musculus - Chlorocebus sabeus - Gallus gallus - Columba livia - Escherichia coli - custom genome(s)

Supported control sequences: - ONT DNA-Seq spike (standard amplicon mapping the 3' end of the Lambda genome) - ONT RNA-Seq spike (yeast ENO2 Enolase II of strain S288C) - Illumina spike (enterobacteria phage phix174) - rRNA database (from https://github.com/biocore/sortmerna/tree/master/data/rRNA_databases) - custom sequence(s)

Align with: - minimap2 - bbduk

- Nextflow
Published by MarieLataretu almost 6 years ago