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biobox/CHANGELOG.md
CI b17c19f92e Build branch main with version main (766ab6c) 
Build pipeline: viash-hub.biobox.main-lpdjj

Source commit: 766ab6c9c3

Source message: Qualimap rnaseq (#74)

* first version

* complete script for qualimap

* add escaping character before leading hashtag (#50)

* add escaping character before leading hashtag

* update changelog

* Update CHANGELOG.md

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* replace escaping \ by \\

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Samtools collate (#49)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.

* Initial commit, whole component is functional

* Update viash (#51)

* update viash

* update readme

* update changelog

* update changelog

* fix incorrect heading detection

* update again

* clean up readme

* Samtools view (#48)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.

* initial version with a few tests, script, and config file

* update changelog, add one test

* add a 4th test, fix option names in the script

* Fix name of component in config

* remove option named with a number

* add must_exist to input file argument

* removed "default: null" from one of the arguments in config

* remove utf8 characters from config

* Update CHANGELOG.md

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Samtools fastq (#52)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.

* Initial commit, config, script, help and test_data

* Update changelog, add tests, fix argument naming errors, add test data

* update changelog, remove gffread namespace field

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* format URL in the description (#55)

* format URL in the description

* update changelog

* Change name in _viash.yaml (#60)

* Update operational code (#63)

* update readme

* switch ci to toolbox

* update to viash 0.9.0-RC6

* edit keywords

* fix version

* update biobox

* cutadapt (#7)

* First commit, clone of cutadapt in htrnaseq + help.txt

* Add config

* Don't allow multiple: true when providing a FASTA file with adapters

* First version of script

* Updates and fixes - se/pe

* Add tests and fix --json argument

* Add software version

* Better consistency in using snake_case

* Update src/cutadapt/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Update src/cutadapt/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Update src/cutadapt/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Specify --input and --input_r2 as separate arguments

* Avoid specifying default arg values

* Add more information to `--minimum_length` and `maximum_length`

* Add --cpus by means of $meta_cpus and set proper default

* Allow multiple for adapters/fasta and add test

* change multiple_sep to ';'

* add example

* simplify code with a helper function

* create directories in test

* use a different output extension if --fasta is provided

* decrease code duplication by separating optional outputs from paired/unpaired output arguments

* write custom tests for cutadapt

* fix _r2 arguments

* add debug flag as not to always print the cli command

* remove comment

* Update to Viash 0.9.0-RC4

* Ability to specify output globbing patterns

* Avoid the need for both output_dir and output

* Move fields from `info` to `links`

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Move references back to the info field

* apologies, I proposed a wrong syntax

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* update changelog

* update readme

* Update salmon quant arguments (#57)

* Make index an optional argument

* FIx argument type and add optional argument

* FEAT: add bedtools getfasta. (#59)

* FEAT: add bedtools getfasta.

* Add PR number to CHANGELOG

* Add star genomegenerate component (#58)

* Add star genomegenerate component

* Update changelog

* Rename component

* Update test

* Update CHANGELOG.md

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* fix package config (#65)

* Delete src/bgzip directory (#64)

It was moved to toolbox

* Output alignments to the transcriptome (#56)

* Output alignments to  the transcriptome

* Change argument name

* BUG: pear component failure is ignored (#70)

* FEAT + BUG: cutadapt; allowing disabling demultiplexing and fix par_quality_cutoff_r2 (#69)

* FEAT: Disable cutadapt demultiplexing by default

* Cutadapt: fix --par_quality_cutoff_r2

* FEAT: update busco to 5.7.1 (#72)

* FEAT: update busco to 5.7.1

* Typo

* Samtools fasta (#53)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.

* Fasta component

* change script resource to samtools_fastq script, with dummy argument to specify the command

* add dummy argument to samtools_fastq to share the script with samtools_fasta

* fix path to script in config

* Update src/samtools/samtools_fastq/script.sh

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Change default fields to examples

* Two more default fields changed to examples

* Minor formatting changes

* Markdown formatting changes in configs

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Umi tools dedup (#54)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.

* inital commit dedup

* Working component with one test

* Update test 1 and test data, fix some arg types in config and script

* test data files and changes to script

* Add third test and test data

* Fix typo in script

* remove utf8 characters in config

* Add choices fields and change default fields to exampels

* Minor formatting changes

* md formatting changes in config

* Fix typo (#79)

* add vscode to gitignore

* update multiple separator (#81)

* update multiple separator

* update changelog

* Update src/multiqc/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Update src/multiqc/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Update src/multiqc/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Update src/multiqc/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* update ifs

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* add test data

* add tests

* update changelog

* remove unrequired test data

* update descriptions

* update changelog

* update help text

* Update src/qualimap/qualimap_rnaseq/script.sh

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* update unit tests

* update unit tests

* addres pr changes request

* add version

* remove whitespace multiqc

* Apply suggestions from code review

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* address pr comments

* Update CHANGELOG.md

* fix doi

* Fix name

* update version and container image

* write software version to file

---------

Co-authored-by: dorien-er <roosen.dorien@gmail.com>
Co-authored-by: Leila011 <leilapaquay@gmail.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: emmarousseau <emmarou1@icloud.com>
Co-authored-by: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com>
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Co-authored-by: Dorien <41797896+dorien-er@users.noreply.github.com>
2024-08-21 11:54:23 +00:00

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biobox x.x.x

BREAKING CHANGES

  • star/star_align_reads: Change all arguments from --camelCase to --snake_case (PR #62).

  • star/star_genome_generate: Change all arguments from --camelCase to --snake_case (PR #62).

NEW FUNCTIONALITY

  • star/star_align_reads: Add star solo related arguments (PR #62).

  • bd_rhapsody/bd_rhapsody_make_reference: Create a reference for the BD Rhapsody pipeline (PR #75).

  • umitools/umitools_dedup: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read (PR #54).

  • seqtk:

    • seqtk/seqtk_sample: Subsamples sequences from FASTA/Q files (PR #68).
    • seqtk/seqtk_subseq: Extract the sequences (complete or subsequence) from the FASTA/FASTQ files based on a provided sequence IDs or region coordinates file (PR #85).

  • agat:

    • agat/agat_convert_sp_gff2gtf: convert any GTF/GFF file into a proper GTF file (PR #76).
    • agat/agat_convert_bed2gff: convert bed file to gff format (PR #97).
    • agat/agat_convert_embl2gff: convert an EMBL file into GFF format (PR #99).
    • agat/agat_convert_sp_gff2tsv: convert gtf/gff file into tabulated file (PR #102).
    • agat/agat_convert_sp_gxf2gxf: fixes and/or standardizes any GTF/GFF file into full sorted GTF/GFF file (PR #103).

  • bedtools:

    • bedtools/bedtools_intersect: Allows one to screen for overlaps between two sets of genomic features (PR #94).
    • bedtools/bedtools_sort: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
    • bedtools/bedtools_bamtofastq: Convert BAM alignments to FASTQ files (PR #101).
    • bedtools/bedtools_bedtobam: Converts genomic feature records (bed/gff/vcf) to BAM format (PR #111).

  • qualimap/qualimap_rnaseq: RNA-seq QC analysis using qualimap (PR #74).

MINOR CHANGES

  • busco components: update BUSCO to 5.7.1 (PR #72).

  • Update CI to reusable workflow in viash-io/viash-actions (PR #86).

  • Update several components in order to avoid duplicate code when using unset on boolean arguments (PR #133).

  • Bump viash to 0.9.0-RC7 (PR #134)

DOCUMENTATION

  • Extend the contributing guidelines (PR #82):

    • Update format to Viash 0.9.

    • Descriptions should be formatted in markdown.

    • Add defaults to descriptions, not as a default of the argument.

    • Explain parameter expansion.

    • Mention that the contents of the output of components in tests should be checked.

  • Add authorship to existing components (PR #88).

BUG FIXES

  • pear: fix component not exiting with the correct exitcode when PEAR fails (PR #70).

  • cutadapt: fix --par_quality_cutoff_r2 argument (PR #69).

  • cutadapt: demultiplexing is now disabled by default. It can be re-enabled by using demultiplex_mode (PR #69).

  • multiqc: update multiple separator to ; (PR #81).

biobox 0.1.0

NEW FEATURES

  • arriba: Detect gene fusions from RNA-seq data (PR #1).

  • fastp: An ultra-fast all-in-one FASTQ preprocessor (PR #3).

  • busco:

    • busco/busco_run: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
    • busco/busco_list_datasets: Lists available busco datasets (PR #18).
    • busco/busco_download_datasets: Download busco datasets (PR #19).

  • cutadapt: Remove adapter sequences from high-throughput sequencing reads (PR #7).

  • featurecounts: Assign sequence reads to genomic features (PR #11).

  • bgzip: Add bgzip functionality to compress and decompress files (PR #13).

  • pear: Paired-end read merger (PR #10).

  • lofreq/call: Call variants from a BAM file (PR #17).

  • lofreq/indelqual: Insert indel qualities into BAM file (PR #17).

  • multiqc: Aggregate results from bioinformatics analyses across many samples into a single report (PR #42).

  • star:

    • star/star_align_reads: Align reads to a reference genome (PR #22).
    • star/star_genome_generate: Generate a genome index for STAR alignment (PR #58).

  • gffread: Validate, filter, convert and perform other operations on GFF files (PR #29).

  • salmon:

    • salmon/salmon_index: Create a salmon index for the transcriptome to use Salmon in the mapping-based mode (PR #24).
    • salmon/salmon_quant: Transcript quantification from RNA-seq data (PR #24).

  • samtools:

    • samtools/samtools_flagstat: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
    • samtools/samtools_idxstats: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
    • samtools/samtools_index: Index SAM/BAM/CRAM files (PR #35).
    • samtools/samtools_sort: Sort SAM/BAM/CRAM files (PR #36).
    • samtools/samtools_stats: Reports alignment summary statistics for a BAM file (PR #39).
    • samtools/samtools_faidx: Indexes FASTA files to enable random access to fasta and fastq files (PR #41).
    • samtools/samtools_collate: Shuffles and groups reads in SAM/BAM/CRAM files together by their names (PR #42).
    • samtools/samtools_view: Views and converts SAM/BAM/CRAM files (PR #48).
    • samtools/samtools_fastq: Converts a SAM/BAM/CRAM file to FASTQ (PR #52).
    • samtools/samtools_fastq: Converts a SAM/BAM/CRAM file to FASTA (PR #53).

  • umi_tools: -umi_tools/umi_tools_extract: Flexible removal of UMI sequences from fastq reads (PR #71).

  • falco: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).

  • bedtools:

    • bedtools_getfasta: extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file (PR #59).

MINOR CHANGES

  • Uniformize component metadata (PR #23).

  • Update to Viash 0.8.5 (PR #25).

  • Update to Viash 0.9.0-RC3 (PR #51).

  • Update to Viash 0.9.0-RC6 (PR #63).

  • Switch to viash-hub/toolbox actions (PR #64).

DOCUMENTATION

  • Update README (PR #64).

BUG FIXES

  • Add escaping character before leading hashtag in the description field of the config file (PR #50).

  • Format URL in biobase/bcl_convert description (PR #55).

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