Merge branch 'main' into rsem

.github/workflows/test.yaml

@@ -1,9 +1,11 @@
-name: Component Testing
+name: Test components
 
 on:
   pull_request:
   push:
+    branches:
+      - main
 
 jobs:
   test:
-    uses: viash-hub/toolbox/.github/workflows/test.yaml@main
+    uses: viash-io/viash-actions/.github/workflows/test.yaml@v6

.gitignore

@@ -3,6 +3,7 @@
 
 # IDE ignores
 .idea/
+.vscode/
 
 # R specific ignores
 .Rhistory

CHANGELOG.md

@@ -1,30 +1,107 @@
 # biobox x.x.x
 
-## NEW FEATURES
-
 * `rsem`:
     - `rsem_calculate_expression`: Calculate expression levels (PR #93).
 
-## BUG FIXES
+* `agat`:
+  - `agat/agat_convert_genscan2gff`: convert a genscan file into a GFF file (PR #100).
+
+* `bd_rhapsody/bd_rhapsody_sequence_analysis`: BD Rhapsody Sequence Analysis CWL pipeline (PR #96).
+
+## MINOR CHANGES
+
+* Upgrade to Viash 0.9.0.
+
+# biobox 0.2.0
+
+## BREAKING CHANGES
+
+* `star/star_align_reads`: Change all arguments from `--camelCase` to `--snake_case` (PR #62).
 
-* `pear`: fix component not exiting with the correct exitcode when PEAR fails.
+* `star/star_genome_generate`: Change all arguments from `--camelCase` to `--snake_case` (PR #62).
 
-* `cutadapt`: fix `--par_quality_cutoff_r2` argument.
+## NEW FUNCTIONALITY
 
-* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
+* `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_genomecov`: Compute the coverage of a feature file (bed/gff/vcf/bam) among a genome (PR #128).
+  - `bedtools/bedtools_groupby`: Summarizes a dataset column based upon common column groupings. Akin to the SQL "group by" command (PR #123).
+  - `bedtools/bedtools_merge`: Merges overlapping BED/GFF/VCF entries into a single interval (PR #118).
+  - `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).
+  - `bedtools/bedtools_bed12tobed6`: Converts BED12 files to BED6 files (PR #140).
+  - `bedtools/bedtools_links`: Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a (bed/gff/vcf) file (PR #137).
+
+* `qualimap/qualimap_rnaseq`: RNA-seq QC analysis using qualimap (PR #74). 
+
+* `rsem/rsem_prepare_reference`: Prepare transcript references for RSEM (PR #89).
+
+* `bcftools`:
+  - `bcftools/bcftools_concat`: Concatenate or combine VCF/BCF files (PR #145).
+  - `bcftools/bcftools_norm`: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows (PR #144).
+  - `bcftools/bcftools_annotate`: Add or remove annotations from a VCF/BCF file (PR #143).
+  - `bcftools/bcftools_stats`: Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats (PR #142).
+  - `bcftools/bcftools_sort`: Sorts BCF/VCF files by position and other criteria (PR #141).
+
+* `fastqc`: High throughput sequence quality control analysis tool (PR #92).
 
 ## MINOR CHANGES
 
-* `busco` components: update BUSCO to `5.7.1`.
+* `busco` components: update BUSCO to `5.7.1` (PR #72).
 
-# biobox 0.1.0
+* Update CI to reusable workflow in `viash-io/viash-actions` (PR #86).
 
-## BREAKING CHANGES
+* Update several components in order to avoid duplicate code when using `unset` on boolean arguments (PR #133).
 
-* Change default `multiple_sep` to `;` (PR #25). This aligns with an upcoming breaking change in
-  Viash 0.9.0 in order to avoid issues with the current default separator `:` unintentionally
-  splitting up certain file paths.
+* 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
 
@@ -73,16 +150,25 @@
     - `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).
+    - `umi_tools/umi_tools_prepareforrsem`: Fix paired-end reads in name sorted BAM file to prepare for RSEM (PR #148).
 
 * `falco`: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).
 
-* `umitools`:
-    - `umitools_dedup`: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read (PR #54).
-
 * `bedtools`:
     - `bedtools_getfasta`: extract sequences from a FASTA file for each of the
                            intervals defined in a BED/GFF/VCF file (PR #59).
 
+* `sortmerna`: Local sequence alignment tool for mapping, clustering, and filtering rRNA from metatranscriptomic 
+               data. (PR #146)
+
+* `fq_subsample`: Sample a subset of records from single or paired FASTQ files (PR #147).
+
+* `kallisto`:
+    - `kallisto_index`: Create a kallisto index (PR #149).
+
+
 ## MINOR CHANGES
 
 * Uniformize component metadata (PR #23).