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Make pretty
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christopher-hakkaart committed Apr 22, 2022
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134 changes: 67 additions & 67 deletions CHANGELOG.md
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Expand Up @@ -7,36 +7,36 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Major enhancements

* Add DNA variant calling functionality
* Add RNA modification and fusion detection functionalities
* Add `demux_fast5` module to output demultiplexed fast5 files when `--output_demultiplex_fast5` is set
* Add `--trim_barcodes` in Guppy basecaller to trim the barcodes from output fastq
* Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
* Removed `--publish_dir_mode` as it is no longer required for the new syntax
* Bump minimum Nextflow version from 21.04.0 -> 21.10.3
* Update pipeline template to nf-core/tools `2.2`
* Update `bambu` version from `1.0.2` to `2.0.0`
* Update `multiqc` version from `1.10.1` to `1.11`
- Add DNA variant calling functionality
- Add RNA modification and fusion detection functionalities
- Add `demux_fast5` module to output demultiplexed fast5 files when `--output_demultiplex_fast5` is set
- Add `--trim_barcodes` in Guppy basecaller to trim the barcodes from output fastq
- Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
- Removed `--publish_dir_mode` as it is no longer required for the new syntax
- Bump minimum Nextflow version from 21.04.0 -> 21.10.3
- Update pipeline template to nf-core/tools `2.2`
- Update `bambu` version from `1.0.2` to `2.0.0`
- Update `multiqc` version from `1.10.1` to `1.11`

### Parameters

* Added `--output_demultiplex_fast5` to output demultiplexed fast5
* Added `--trim_barcodes` in Guppy basecaller to trim the barcodes from output fastq
* Added `--call_variants` to detect DNA variants
* Added `--split_mnps` to split multi-nucleotide polymorphisms into single nucleotide polymorphisms
* Added `--phase_vcf` to output a phased vcf
* Added `--skip_medaka` to skip `medaka_variant`
* Added `--skip_sniffles` to skip `sniffles`
* Added `--skip_modification_analysis` to skip RNA modification detection
* Added `--skip_xpore` to skip `xpore`
* Added `--skip_m6anet` to skip `m6anet`
* Added `--skip_fusion_analysis` to skip RNA fusion detection
* Added `--jaffal_ref_dir` to indicate the reference directory path required by `JAFFAL`
- Added `--output_demultiplex_fast5` to output demultiplexed fast5
- Added `--trim_barcodes` in Guppy basecaller to trim the barcodes from output fastq
- Added `--call_variants` to detect DNA variants
- Added `--split_mnps` to split multi-nucleotide polymorphisms into single nucleotide polymorphisms
- Added `--phase_vcf` to output a phased vcf
- Added `--skip_medaka` to skip `medaka_variant`
- Added `--skip_sniffles` to skip `sniffles`
- Added `--skip_modification_analysis` to skip RNA modification detection
- Added `--skip_xpore` to skip `xpore`
- Added `--skip_m6anet` to skip `m6anet`
- Added `--skip_fusion_analysis` to skip RNA fusion detection
- Added `--jaffal_ref_dir` to indicate the reference directory path required by `JAFFAL`

### Software dependencies

| Dependency | Old version | New version |
|-------------------------|-------------|-------------|
| ----------------------- | ----------- | ----------- |
| `bioconductor-bambu` | 1.0.2 | 2.0.0 |
| `bioconductor-bsgenome` | 1.58.0 | 1.62.0 |
| `guppy` | 4.0.14 | 5.0.16 |
Expand All @@ -50,77 +50,77 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Bug fix

* The `GET_TEST_DATA` process now uses checks for any file in the path.
- The `GET_TEST_DATA` process now uses checks for any file in the path.

> **NB:** Dependency has been __updated__ if both old and new version information is present.
> **NB:** Dependency has been __added__ if just the new version information is present.
> **NB:** Dependency has been __removed__ if version information isn't present.
> **NB:** Dependency has been **updated** if both old and new version information is present.
> **NB:** Dependency has been **added** if just the new version information is present.
> **NB:** Dependency has been **removed** if version information isn't present.
## [2.0.1] - 2021-11-29

### Bug fix

* The `UCSC_BEDGRAPHTOBIGWIG` process now uses the `ucsc-bedgraphtobigwig` container
* The full-size and minimal AWS tests have successfully finished after changing to the `ucsc-bedgraphtobigwig` container
- The `UCSC_BEDGRAPHTOBIGWIG` process now uses the `ucsc-bedgraphtobigwig` container
- The full-size and minimal AWS tests have successfully finished after changing to the `ucsc-bedgraphtobigwig` container

## [2.0.0] - 2021-11-26

### Major enhancements

* Pipeline has been re-implemented in [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
* Software containers are now obtained from [Biocontainers](https://biocontainers.pro/#/registry)
* Update pipeline template to nf-core/tools `2.1`
* [#77](https://github.com/nf-core/nanoseq/issues/77) - Skipped alignment steps
* [#97](https://github.com/nf-core/nanoseq/issues/97) - Add optional DNA cleaning option
- Pipeline has been re-implemented in [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
- Software containers are now obtained from [Biocontainers](https://biocontainers.pro/#/registry)
- Update pipeline template to nf-core/tools `2.1`
- [#77](https://github.com/nf-core/nanoseq/issues/77) - Skipped alignment steps
- [#97](https://github.com/nf-core/nanoseq/issues/97) - Add optional DNA cleaning option

### Parameters

* Added `--run_nanolyse` to run NanoLyse for DNA cleaning of FastQ files
* Added `--nanolyse_fasta` to provide a fasta file for nanolyse to filter against
- Added `--run_nanolyse` to run NanoLyse for DNA cleaning of FastQ files
- Added `--nanolyse_fasta` to provide a fasta file for nanolyse to filter against

### Software dependencies

| Dependency | Old version | New version |
|-------------------------|-------------|-------------|
| `bioconductor-bambu` | 1.0.0 | 1.0.2 |
| `nanolyse` | | 1.2.0 |
| `r-base` | 4.0.3 | 4.0.2 |
| Dependency | Old version | New version |
| -------------------- | ----------- | ----------- |
| `bioconductor-bambu` | 1.0.0 | 1.0.2 |
| `nanolyse` | | 1.2.0 |
| `r-base` | 4.0.3 | 4.0.2 |

> **NB:** Dependency has been __updated__ if both old and new version information is present.
> **NB:** Dependency has been __added__ if just the new version information is present.
> **NB:** Dependency has been __removed__ if version information isn't present.
> **NB:** Dependency has been **updated** if both old and new version information is present.
> **NB:** Dependency has been **added** if just the new version information is present.
> **NB:** Dependency has been **removed** if version information isn't present.
## [1.1.0] - 2020-11-06

### Major enhancements

* Transcript reconstruction and quantification ([`bambu`](https://bioconductor.org/packages/release/bioc/html/bambu.html) or [`StringTie2`](https://ccb.jhu.edu/software/stringtie/) and [`featureCounts`](http://bioinf.wehi.edu.au/featureCounts/))
* Differential expression analysis at the gene-level ([`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)) and transcript-level ([`DEXSeq`](https://bioconductor.org/packages/release/bioc/html/DEXSeq.html))
* Ability to provide BAM input to the pipeline
* Change samplesheet format to be more flexible to BAM input files
* Add pycoQC and featureCounts output to MultiQC report
* Add AWS full-sized test data
* Add parameter JSON schema for pipeline
* Add citations file
* Update pipeline template to nf-core/tools `1.11`
* Collapsible sections for output files in `docs/output.md`
* Replace `set` with `tuple` and `file` with `path` in `input` section of all processes
* Capitalise process names
* Added `--gpus all` to Docker `runOptions` when using GPU as mentioned [here](https://github.com/docker/compose/issues/6691#issuecomment-514429646)
* Cannot invoke method `containsKey()` on null object when `--igenomes_ignore` is set [#76](https://github.com/nf-core/nanoseq/issues/76)
- Transcript reconstruction and quantification ([`bambu`](https://bioconductor.org/packages/release/bioc/html/bambu.html) or [`StringTie2`](https://ccb.jhu.edu/software/stringtie/) and [`featureCounts`](http://bioinf.wehi.edu.au/featureCounts/))
- Differential expression analysis at the gene-level ([`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)) and transcript-level ([`DEXSeq`](https://bioconductor.org/packages/release/bioc/html/DEXSeq.html))
- Ability to provide BAM input to the pipeline
- Change samplesheet format to be more flexible to BAM input files
- Add pycoQC and featureCounts output to MultiQC report
- Add AWS full-sized test data
- Add parameter JSON schema for pipeline
- Add citations file
- Update pipeline template to nf-core/tools `1.11`
- Collapsible sections for output files in `docs/output.md`
- Replace `set` with `tuple` and `file` with `path` in `input` section of all processes
- Capitalise process names
- Added `--gpus all` to Docker `runOptions` when using GPU as mentioned [here](https://github.com/docker/compose/issues/6691#issuecomment-514429646)
- Cannot invoke method `containsKey()` on null object when `--igenomes_ignore` is set [#76](https://github.com/nf-core/nanoseq/issues/76)

### Parameters

* Added `--barcode_both_ends` requires barcode on both ends for Guppy basecaller
* Added `--quantification_method` to specify the transcript quantification method to use
* Added `--skip_quantification` to skip transcript quantification and differential analysis
* Added `--skip_differential_analysis` to skip differential analysis with DESeq2 and DEXSeq
* Added `--publish_dir_mode` to customise method of publishing results to output directory [nf-core/tools#585](https://github.com/nf-core/tools/issues/585)
- Added `--barcode_both_ends` requires barcode on both ends for Guppy basecaller
- Added `--quantification_method` to specify the transcript quantification method to use
- Added `--skip_quantification` to skip transcript quantification and differential analysis
- Added `--skip_differential_analysis` to skip differential analysis with DESeq2 and DEXSeq
- Added `--publish_dir_mode` to customise method of publishing results to output directory [nf-core/tools#585](https://github.com/nf-core/tools/issues/585)

### Software dependencies

| Dependency | Old version | New version |
|-------------------------|-------------|-------------|
| ----------------------- | ----------- | ----------- |
| `Guppy` | 3.4.4 | 4.0.14 |
| `markdown` | 3.1.1 | 3.3.3 |
| `multiqc` | 1.8 | 1.9 |
Expand All @@ -143,9 +143,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| `subread` | - | 2.0.1 |
| `psutil` | - | - |

> **NB:** Dependency has been __updated__ if both old and new version information is present.
> **NB:** Dependency has been __added__ if just the new version information is present.
> **NB:** Dependency has been __removed__ if version information isn't present.
> **NB:** Dependency has been **updated** if both old and new version information is present.
> **NB:** Dependency has been **added** if just the new version information is present.
> **NB:** Dependency has been **removed** if version information isn't present.
## [1.0.0] - 2020-03-05

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