htrnaseq/CHANGELOG.md

htrnaseq v0.9.1

Bug fixes

• Reverted functionality to set fastq_publish_dir and results_publish_dir using fromState (PR #64).

• runner: fix detection of FASTQ files with non-numerical characters in the sample name (PR #65).

htrnaseq v0.9.0

Breaking changes

• runner: removed plain_output argument (PR #63).

Minor changes

• runner: the fastq_publish_dir and results_publish_dir can now be set using fromState when using the workflow as subworkflow (PR #63).

htrnaseq v0.8.3

Minor changes

• Bump craftbox to v0.2.0 (PR #62).

htrnaseq v0.8.2

Under the hood

• Add the package config (_viash.yaml) to every component's target dir. This makes introspection from, e.g. a runner workflow much more robust (PR #61)

htrnaseq v0.8.1

Bug fixes

• Fix an issue where the FASTQ files from different samples on the same sequencing run would overwrite each other (PR #56).

Under the hood

• Moved the test resources to their new location (PR #47).

Minor changes

• Bump biobox and craftbox dependencies to versions 0.3.1 and 0.2.0, respectively (PR #60).

htrnaseq v0.8.0

New functionality

• save_params: added a component to save workflow input parameters as yaml (PR #48).

• Added run_params parameter to htrnaseq and runner workflows in order to save the input parameters used for the workflow run (PR #48).

htrnaseq v0.7.2

Documentation

• Update README (PR #54)

htrnaseq v0.7.1

Bug fixes

• Bump viash version to 0.9.4. This adds support for nextflow versions starting major version 25.01 and fixes an issue where an integer being passed to a argument with type: double resulted in an error (PR #51).

• reporting: updated default colour mapping (PR #50).

Minor changes

• create_report: bump bioconductor version to 3.21 in order to accommodate R version 4.5 (PR #52).

htrnaseq v0.7.0

Breaking changes

The runner and htrnaseq workflow now output FASTQ files corresponding to the barcodes per input ID (per sequencing run). Previously, when multiple input folders or multiple input FASTQ files were provided (for the runner and htrnaseq workflows respectively), the demultiplexed FASTQ files for these inputs were concatenated and provided as output. For the htrnaseq workflow, reads can still be combined by using a newly added sampleID argument. This means that two lists of FASTQ files can be provided for a single sample, and by assigning the same sampleID, these reads will be joined. For example, with other arguments are left out for brevity:

- id: sample1_run1
  input_r1: [sample_1_L001_1_R1.fastq, sample_1_L002_1_R1.fastq]
  input_r2: [sample_1_L001_1_R2.fastq, sample_1_L002_1_R2.fastq]
  sampleID: "sample_1"
- id: sample1_run2
  input_r1: [sample_1_L001_1_R1.fastq, sample_1_L002_1_R1.fastq]
  input_r2: [sample_1_L001_1_R2.fastq, sample_1_L002_1_R2.fastq]
  sampleID: "sample_1"
- id: sample_2
  input_r1: [sample_2_L001_1_R1.fastq, sample_2_L002_1_R1.fastq]
  input_r2: [sample_2_L001_1_R2.fastq, sample_2_L002_1_R2.fastq]

For the runner, concatenation of data across samples is automatically inferred. Previously, multiple IDs (events) could be provided which were processed in parallel. This is no longer possible, as providing multiple will cause the matching samples for these runs to be concatenated.

For example, the following old parameter yaml

- id: run1
  input: ["run_folder_1/", run_folder_2/]

should now be provided as:

- id: run1
  input: "run_folder_1/"
- id: run2
  input: run_folder_2/

Minor changes

• Updated viash to 0.9.2 (PR #49)

htrnaseq v0.6.0

Breaking changes

• runner: a subdirectory data_processed is now added to the output structure, in between the experiment ID and the directory with the workflow date and version (PR #45).

htrnaseq v0.5.5

New functionality

• Add umi_length parameter to the runner workflow (PR #46)

htrnaseq v0.5.4

• Fix missing barcodes in the output from generate_pool_statistics, which caused an assertion error in create_pdata. In order to resolve the issue generate_well_statistics now outputs results for all chromosomes/scaffolds presented by the genome annotation, even when no reads were mapped to the regions in question. generate_pool_statistics will now remove regions from the output that have not at least one counts across all barcodes (PR #44).

htrnaseq v0.5.3

Bug fixes

• Fix create_eset component failing to create when one of the input samples has no counts (PR #43).

htrnaseq v0.5.2

Bug fixes

• create_fdata: remove duplicate entries from feature data (PR #41).

htrnaseq v0.5.1

Bug fixes

• generate_well_statistics: fix ValueError when an empty .bam file is provided as input (PR #40).
• create_pdata: avoid false positive ValueError for non-overlapping barcodes when input data contains empty (NA) values (PR #40).

htrnaseq v0.5.0

New functionality

• Added ignore parameter was added to the runner workflow in order to pass over certain input files from the input directory (PR #39).

htrnaseq v0.4.0

Breaking changes

An effort has been made to align the inputs for the htrnaseq and the mapping and demultiplexing of the wells, in order simplify running these steps as seperate steps (PR #37).

• Changes to the parallel_map component:
  • The barcode argument has been renamed to barcodesFasta and the provided value for this argument must now be single FASTA file instead of a list of barcodes.
  • The filenames for the provided FASTQ files must now conform to the format {name}_R(1|2).fasta, where {name} is the well identifiers. The well identifiers correspond to the headers of the FASTA file containing the barcodes (up untill the first whitespace). Forward and reverse FASTQ files must still be provided in pairs, meaning that the order of files provided to input_r1 and input_r2 remains important.
  • The requirement for equal number of barcodes and FASTQ pairs to be provided has been dropped. Instead, the barcodes provided with barcodesFasta are matched to the input FASTQ files by comparing the header of the FASTA records to the file names of the provided FASTQ input files. Each barcode must match exactly one FASTQ input pair (forward and reverse reads), but FASTQ files that were not matched to any barcode are not processed. Basically, the barcodes fasta can now act as a filter for the FASTQ files to be mapped.
• The utils/groupWells workflow has been removed.
• parallel_map_wf has been removed as its functionality is now incomporated into the parallel_map component.
• The pool, well_id, barcode, lane, pair_end and n_wells output arguments have been dropped from the well_demultiplexing workflow. This workflow now only outputs a list of demultiplexed FASTQ files.
• A well_metadata workflow has been implemented that extracts the metadata that is no longer output by the well_demultiplexing workflow from the demultiplexed files and the barcodes FASTA.

New functionality

• Multiple input directories can not be provided. The input reads from these from these directories will be joined per barcode before mapping. This is useful when data has been generated using multiple sequencing runs in order to increase sequencing depth (PR #38).

htrnaseq v0.3.0

New functionality

• Added umi_length argument (PR #27).
• Added runner workflow (PR #26, see below)

runner workflow

• Removed wellBarcodesLength from parallel_map workflow (PR #27).

Major changes

A runner workflows has been added, providing two additional features:

1. Start from an input directory containing fastq files rather than a list of input fastq pairs.
2. Improve the output of the workflow

Input directory

It is now possible to specify a single --input <basedir> directory as input and the runner will extract the fastq file pairs. An error will be raised if the filename processing leads to errors.

Output

The runner provides a complete different approach to output. A couple of things are important here:

• Output is split up in 2 parts:

  1. The well-demultiplexed fastq files (--fastq_publish_dir)
  2. All the other results of the workflow (--results_publish_dir)

• The well-demultiplexed fastq file are stored under --fastq_publish_dir according to the following format:

  $fastq_publish_dir/$id/<date-time>_htrnaseq_<version>/$plate_$lane/<well_id>_R1/2_001.fastq
  

• The other results are stored under --results_publish_dir according to the following format:

  $results_publish_dir/$project_id/$experiment_id/<date-time>_htrnaseq_<version>/
  

  This is an example listing of this directory:

  esets
  fData
  nrReadsNrGenesPerChrom
  pData
  report.html
  star_output
  starLogs
  

This output structure can be circumvented by using the --output_dir option, which will store all output in a single directory.

1. Using the htrnaseq workflow directory rather than the runner interface
2. Using the argument --plain_output with the runner. fastq files and other results will still be published in their respective directories, but not in a directory hierarchy as described above.

Minor changes

• Use v0.2.0 version of cutadapt instead of main (PR #23).
• Use v0.3.0 version of cutadapt
• Bump viash to 0.9.1 (PR #31).
• create_eset: Update base container image, R version and all dependencies to newer versions (PR #28).

htrnaseq v0.2.0

New functionality

• Make sure that the Well ID matches the required format (PR #22 and PR #21).

htrnaseq v0.1.0

Initial release