From ecbf5403698dc0ee9c51e5974ef20d616ab8b3f3 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 5 Jul 2024 11:42:43 +1000 Subject: [PATCH 1/8] Include 1.0.0 version in release parity table --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 926ca174..994263c5 100644 --- a/README.md +++ b/README.md @@ -111,14 +111,14 @@ Versions nominated to have current long-term support: ### Release parity -Versioning between oncoanalyser and hmftools naturally differ, however it is often necessary to relate the functional +Versioning between `oncoanalyser` and hmftools naturally differ, however it is often necessary to relate the functional equivalence of these two pieces of software. The functional/feature parity with regards to version releases are detailed in the below table. | oncoanalyser | hmftools | | ------------------- | -------- | | 0.1.0 through 0.2.7 | 5.33 | -| 0.3.0 through 0.4.5 | 5.34 | +| 0.3.0 through 1.0.0 | 5.34 | ## Known issues From d36f8b059743d421ad864cfbbc2378029edcba00 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 5 Jul 2024 11:43:20 +1000 Subject: [PATCH 2/8] Remove TODO in methods_description_template.yml --- assets/methods_description_template.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 6bb8cb5b..822724fb 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/oncoanalyser Methods Description" section_href: "https://github.com/nf-core/oncoanalyser" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

Data was processed using nf-core/oncoanalyser v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

From dcf919e8d87426860d027e7fa8a8729b23ef10c5 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 5 Jul 2024 11:43:41 +1000 Subject: [PATCH 3/8] Adjust filepaths in assets/samplesheet.csv --- assets/samplesheet.csv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 157d28bf..1a8d4b39 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,12 +1,12 @@ group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath -subject_one__to__dna,subject_one,sample_a,tumor,dna,bam,/Users/stephen/repos/oncoanalyser/subject_one/sample_a.tumor.bam +subject_one__to__dna,subject_one,sample_a,tumor,dna,bam,/path/to/subject_one/sample_a.tumor.bam -subject_one__tn__dna,subject_one,sample_a,tumor,dna,bam,/Users/stephen/repos/oncoanalyser/subject_one/sample_a.tumor.bam -subject_one__tn__dna,subject_one,sample_b,normal,dna,bam,/Users/stephen/repos/oncoanalyser/subject_one/sample_b.normal.bam +subject_one__tn__dna,subject_one,sample_a,tumor,dna,bam,/path/to/subject_one/sample_a.tumor.bam +subject_one__tn__dna,subject_one,sample_b,normal,dna,bam,/path/to/subject_one/sample_b.normal.bam -subject_one__tn__dna_rna,subject_one,sample_a,tumor,dna,bam,/Users/stephen/repos/oncoanalyser/subject_one/sample_a.tumor.bam -subject_one__tn__dna_rna,subject_one,sample_b,normal,dna,bam,/Users/stephen/repos/oncoanalyser/subject_one/sample_b.normal.bam -subject_one__tn__dna_rna,subject_one,sample_c,tumor,rna,bam,/Users/stephen/repos/oncoanalyser/subject_one/sample_c.tumor_rna.bam +subject_one__tn__dna_rna,subject_one,sample_a,tumor,dna,bam,/path/to/subject_one/sample_a.tumor.bam +subject_one__tn__dna_rna,subject_one,sample_b,normal,dna,bam,/path/to/subject_one/sample_b.normal.bam +subject_one__tn__dna_rna,subject_one,sample_c,tumor,rna,bam,/path/to/subject_one/sample_c.tumor_rna.bam -subject_one__to__dna_rna,subject_one,sample_a,tumor,dna,bam,/Users/stephen/repos/oncoanalyser/subject_one/sample_a.tumor.bam -subject_one__to__dna_rna,subject_one,sample_c,tumor,rna,bam,/Users/stephen/repos/oncoanalyser/subject_one/sample_c.tumor_rna.bam +subject_one__to__dna_rna,subject_one,sample_a,tumor,dna,bam,/path/to/subject_one/sample_a.tumor.bam +subject_one__to__dna_rna,subject_one,sample_c,tumor,rna,bam,/path/to/subject_one/sample_c.tumor_rna.bam From dd4f868e81c2c4ba29b2d7661da15592b32ce72c Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 5 Jul 2024 11:44:12 +1000 Subject: [PATCH 4/8] Simplify target parameter definitions --- conf/targeted_parameters.config | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/conf/targeted_parameters.config b/conf/targeted_parameters.config index bb4899e7..c02575be 100644 --- a/conf/targeted_parameters.config +++ b/conf/targeted_parameters.config @@ -1,6 +1,4 @@ -process.'withName:^.*:COBALT_PROFILING:COBALT'.ext.args = [ - '-pcf_gamma 50', -].join(' ').trim() +process.'withName:^.*:COBALT_PROFILING:COBALT'.ext.args = '-pcf_gamma 50' process.'withName:^.*:SAGE_CALLING:SOMATIC'.ext.args = [ '-high_depth_mode', From 882cb6c68f4060da3307cb6b70da27ca27f1c51e Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 5 Jul 2024 11:44:58 +1000 Subject: [PATCH 5/8] Fix templated version in usage.md --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index d0677b8f..9cbcb2a0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -214,7 +214,7 @@ nextflow pull nf-core/oncoanalyser It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [nf-core/oncoanalyser releases page](https://github.com/nf-core/oncoanalyser/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. +First, go to the [nf-core/oncoanalyser releases page](https://github.com/nf-core/oncoanalyser/releases) and find the latest pipeline version - numeric only (eg. `1.0.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.0.0`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. From 204d75bfd8981922ef8e763101ccf4f779139a59 Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 5 Jul 2024 11:46:15 +1000 Subject: [PATCH 6/8] Fix grammar and clarify usage.md --- docs/usage.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 9cbcb2a0..fbbb7a0f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -229,7 +229,7 @@ If you wish to share such profile (such as upload as supplementary material for ### Selecting processes Most of the major components in oncoanalyser can be skipped using `--processes_exclude` (the full list of available -processes can be view [here](https://github.com/nf-core/oncoanalyser/blob/1.0.0/lib/Constants.groovy#L36-L56)). +processes can be viewed [here](https://github.com/nf-core/oncoanalyser/blob/1.0.0/lib/Constants.groovy#L36-L56)). Multiple processes can be given as a comma-separated list. While there are some use-cases for this feature (e.g. skipping resource intensive processes such as VIRUSBreakend), it becomes more powerful when combined with existing inputs as described in the following section. @@ -243,10 +243,11 @@ processes. ### Existing inputs -The oncoanalyser pipeline has been designed to allow entry at arbitrary points, which is particularly useful in -situations where previous outputs exist and re-running oncoanalyser is desired (e.g. to subsequently execute an -optional sensor or use an upgrade component such as PURPLE). The primary advantage of this approach is that only the -required processes are executed, reducing costs and runtimes by skipping unnecessary processes. +The `oncoanalyser` pipeline has been designed to allow entry at arbitrary points, which is particularly useful in +situations where previous outputs exist and re-running `oncoanalyser` is desired (e.g. to subsequently execute an +optional sensor/workflow or re-run an analysis with an upgraded tool such as PURPLE). The primary advantage of this +approach is that only the required processes are executed, reducing costs and runtimes by skipping unnecessary +processes. In order to effectively utilise this feature, existing inputs must be set in the [samplesheet](#samplesheet) and the appropriate [processes selected](#selecting-processes). Take the below example where existing PURPLE inputs are used so From 02431cae8e79bcec9f1ab6aadd9a748a5fd7badd Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 5 Jul 2024 11:48:58 +1000 Subject: [PATCH 7/8] Add backticks to in text usage of oncoanalyser --- README.md | 10 +++++----- docs/output.md | 4 ++-- docs/usage.md | 36 ++++++++++++++++++------------------ 3 files changed, 25 insertions(+), 25 deletions(-) diff --git a/README.md b/README.md index 994263c5..f0e49dc0 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ For detailed information on each component of the Hartwig workflow, please refer ## Pipeline summary -The following processes and tools can be run with oncoanalyser: +The following processes and tools can be run with `oncoanalyser`: - Simple DNA/RNA alignment (`bwa-mem2`, `STAR`) - Post-alignment processing (`MarkDups`, `Picard MarkDuplicates`) @@ -69,7 +69,7 @@ P1__wgts,P1,SB,tumor,dna,fastq,library_id:SB_library;lane:001,/path/to/SB.tumor. P1__wgts,P1,SC,tumor,rna,fastq,library_id:SC_library;lane:001,/path/to/SC.tumor.rna.wts.001.R1.fastq.gz;/path/to/SC.tumor.rna.wts.001.R2.fastq.gz ``` -Launch oncoanalyser: +Launch `oncoanalyser`: ```bash nextflow run nf-core/oncoanalyser \ @@ -96,7 +96,7 @@ For more details about the output files and reports, please refer to the ### Extended support -As oncoanalyser is used in clinical settings and subject to accreditation standards in some instances, there is a need +As `oncoanalyser` is used in clinical settings and subject to accreditation standards in some instances, there is a need for long-term stability and reliability for feature releases in order to meet operational requirements. This is accomplished through long-term support of several nominated feature releases, which all receive bug fixes and security fixes during the period of extended support. @@ -126,7 +126,7 @@ There are currently no known issues. ## Credits -The oncoanalyser pipeline was written by Stephen Watts while in the [Genomics Platform +The `oncoanalyser` pipeline was written by Stephen Watts while in the [Genomics Platform Group](https://mdhs.unimelb.edu.au/centre-for-cancer-research/our-research/genomics-platform-group) at the [University of Melbourne Centre for Cancer Research](https://mdhs.unimelb.edu.au/centre-for-cancer-research). @@ -146,7 +146,7 @@ channel](https://nfcore.slack.com/channels/oncoanalyser) (you can join with [thi ## Citations -You can cite the oncoanalyser zenodo record for a specific version using the following doi: +You can cite the `oncoanalyser` zenodo record for a specific version using the following doi: [10.5281/zenodo.XXXXXXX](https://doi.org/10.5281/zenodo.XXXXXXX) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) diff --git a/docs/output.md b/docs/output.md index e2a75b72..d1cdfb15 100644 --- a/docs/output.md +++ b/docs/output.md @@ -78,13 +78,13 @@ output/ ### Simple DNA/RNA alignment -Alignment functionality in oncoanalyser is simple and rigid, and exists only to meet the exact requirements of the +Alignment functionality in `oncoanalyser` is simple and rigid, and exists only to meet the exact requirements of the hmftools. #### bwa-mem2 [bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) is a short-read mapping tool used to align reads to a large reference -sequences. In oncoanalyser, bwa-mem2 is used to align DNA reads to the human genome. +sequences. In `oncoanalyser`, bwa-mem2 is used to align DNA reads to the human genome. _No outputs are published directly from bwa-mem2, see [MarkDups](#markdups) for the fully processed alignment outputs_ diff --git a/docs/usage.md b/docs/usage.md index fbbb7a0f..ebc975ba 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,20 +6,20 @@ ## Introduction -The oncoanalyser pipeline typically runs from FASTQs or BAMs and supports two modes: (1) whole genome and/or +The `oncoanalyser` pipeline typically runs from FASTQs or BAMs and supports two modes: (1) whole genome and/or transcriptome, and (2) targeted panel. Launching an analysis requires only the creation of a samplesheet that describes details of each input such as the sample type (tumor or normal), sequence type (DNA or RNA), and filepath. -Various aspects of an oncoanalyser analysis can be configured to fit a range of needs, and many of these are considered -[advanced usage](#advanced-usage) of the pipeline. The most useful include: +Various aspects of an `oncoanalyser` analysis can be configured to fit a range of needs, and many of these are +considered [advanced usage](#advanced-usage) of the pipeline. The most useful include: - precise process selection - starting from existing data - granular control over reference/resource files -These features enable oncoanalyser to be run in a highly flexible way. For example, an analysis can be run with existing -PURPLE data as the starting point and skip variant calling processes. Additionally, reference/resource files can be -staged locally to optimise execution or modified to create user-defined driver gene panels. +These features enable `oncoanalyser` to be run in a highly flexible way. For example, an analysis can be run with +existing PURPLE data as the starting point and skip variant calling processes. Additionally, reference/resource files +can be staged locally to optimise execution or modified to create user-defined driver gene panels. :::danger @@ -35,7 +35,7 @@ When starting from BAMs rather than FASTQ it is expected that: ## Supported analyses -A variety of analyses are accessible in oncoanalyser and are implicitly run according to the data described in the +A variety of analyses are accessible in `oncoanalyser` and are implicitly run according to the data described in the samplesheet. The supported analysis types for each workflow are listed below. | Input sequence data | WGS/WTS workflow | Targeted sequencing workflow\* | @@ -50,7 +50,7 @@ samplesheet. The supported analysis types for each workflow are listed below. ## Samplesheet -A samplesheet that contains information of each input in CSV format is needed to run oncoanalyser. The required input +A samplesheet that contains information of each input in CSV format is needed to run `oncoanalyser`. The required input details and columns are [described below](#column-descriptions). Several different input filetypes beyond FASTQ and BAM are recognised, including intermediate output files generated @@ -157,7 +157,7 @@ This will launch the pipeline with the `docker` configuration profile. See below :::note -Reference data will be retrieved by oncoanalyser for every analysis run. It is therefore strongly recommended when +Reference data will be retrieved by `oncoanalyser` for every analysis run. It is therefore strongly recommended when running multiple analyses to pre-stage reference data locally to avoid it being retrieved multiple times. See [Staging reference data](#staging-reference-data). @@ -228,7 +228,7 @@ If you wish to share such profile (such as upload as supplementary material for ### Selecting processes -Most of the major components in oncoanalyser can be skipped using `--processes_exclude` (the full list of available +Most of the major components in `oncoanalyser` can be skipped using `--processes_exclude` (the full list of available processes can be viewed [here](https://github.com/nf-core/oncoanalyser/blob/1.0.0/lib/Constants.groovy#L36-L56)). Multiple processes can be given as a comma-separated list. While there are some use-cases for this feature (e.g. skipping resource intensive processes such as VIRUSBreakend), it becomes more powerful when combined with existing @@ -262,7 +262,7 @@ P1__wgts,P1,SB,tumor,dna,purple_dir,/path/to/P1.purple_dir/ :::note -The original source input file (i.e. BAM or FASTQ) must always be provided for oncoanalyser to infer the correct +The original source input file (i.e. BAM or FASTQ) must always be provided for `oncoanalyser` to infer the correct analysis type. ::: @@ -282,7 +282,7 @@ nextflow run nf-core/oncoanalyser \ :::warning -Providing existing inputs will cause oncoanalyser to skip the corresponding process but _not any_ of the upstream +Providing existing inputs will cause `oncoanalyser` to skip the corresponding process but _not any_ of the upstream processes. It is the responsibility of the user to skip all relevant processes. ::: @@ -316,7 +316,7 @@ params { } ``` -To use these hmftools resource file overrides in oncoanalyser the local bundle directory must be provided with +To use these hmftools resource file overrides in `oncoanalyser` the local bundle directory must be provided with `--ref_data_hmf_data_path`. #### Customise other data @@ -327,8 +327,8 @@ for the complete list. #### Staging reference data -Default reference data can be staged locally with oncoanalyser by providing a samplesheet for the desired analysis and -setting the `--prepare_reference_only` argument. The samplesheet and oncoanalyser configuration will determine the +Default reference data can be staged locally with `oncoanalyser` by providing a samplesheet for the desired analysis and +setting the `--prepare_reference_only` argument. The samplesheet and `oncoanalyser` configuration will determine the relevant reference data to download. For example the following command will download the `GRCh38_hmf` genome plus indices, reference data, and databases required to run a WGTS analysis for tumor/normal DNA with tumor RNA: @@ -354,7 +354,7 @@ Executing the above command will download and unpack default reference data with complete the prepared reference files can found in `./prepare_reference/reference_data/1.0.0//`. It is recommended to remove the Nextflow work directory after staging data to free disk space. -For oncoanalyser to use locally staged reference data a custom config can be used: +For `oncoanalyser` to use locally staged reference data a custom config can be used: ```text title="refdata.local.config" params { @@ -429,13 +429,13 @@ params { } ``` -Each index required for the analysis will first be created before running the rest of oncoanalyser with the following +Each index required for the analysis will first be created before running the rest of `oncoanalyser` with the following command: :::note In a process similar to [staging reference data](#staging-reference-data), you can first generate the required indexes -by setting `--prepare_reference_only` and then provide the prepared reference files to oncoanalyser through a custom +by setting `--prepare_reference_only` and then provide the prepared reference files to `oncoanalyser` through a custom config file. This avoids having to regenerate indexes for each new analysis. ::: From bbf66f6c46ac8aa20d022cd8e68c453ff05ec71e Mon Sep 17 00:00:00 2001 From: Stephen Watts Date: Fri, 5 Jul 2024 11:59:48 +1000 Subject: [PATCH 8/8] Update .bumpversion.cfg --- .bumpversion.cfg | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index eb4c5b1c..079dcdaa 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -9,5 +9,17 @@ search = version = '{current_version}' replace = version = '{new_version}' [bumpversion:file:README.md] -search = -revision v{current_version} -replace = -revision v{new_version} +search = -revision {current_version} +replace = -revision {new_version} + +[bumpversion:file (example commands):docs/usage.md] +search = -revision {current_version} +replace = -revision {new_version} + +[bumpversion:file (urls):docs/usage.md] +search = /{current_version}/ +replace = /{new_version}/ + +[bumpversion:file (templated example):docs/usage.md] +search = {current_version}` +replace = {new_version}`