Skip to content
Snippets Groups Projects
Commit bee153c4 authored by nservant's avatar nservant
Browse files

prettier

parent 29d8e1f4
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
CHANGELOG.md
+ 12
− 11
View file @ bee153c4
......@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## v1.4.0
### `Added`
* DSL2 version of nf-core-hic pipeline
## v1.3.1 - 2021-09-25
......@@ -75,21 +76,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
* cooler `0.8.5` > `0.8.6`
* multiqc `1.7` > `1.8`
* iced `0.5.1` > `0.5.6`
* *_New_* pymdown-extensions `7.1`
* *_New_* hicexplorer `3.4.3`
* *_New_* bioconductor-hitc `1.32.0`
* *_New_* r-optparse `1.6.6`
* *_New_* ucsc-bedgraphtobigwig `377`
* *_New_* cython `0.29.19`
* *_New_* cooltools `0.3.2`
* *_New_* fanc `0.8.30`
* *_Removed_* r-markdown
* _*New*_ pymdown-extensions `7.1`
* _*New*_ hicexplorer `3.4.3`
* _*New*_ bioconductor-hitc `1.32.0`
* _*New*_ r-optparse `1.6.6`
* _*New*_ ucsc-bedgraphtobigwig `377`
* _*New*_ cython `0.29.19`
* _*New*_ cooltools `0.3.2`
* _*New*_ fanc `0.8.30`
* _*Removed*_ r-markdown
### `Fixed`
* Fix error in doc for Arima kit usage
* Sort output of `get_valid_interaction` process as the input files of `remove_duplicates`
are expected to be sorted (sort -m)
are expected to be sorted (sort -m)
### `Deprecated`
......@@ -138,7 +139,7 @@ DNase Hi-C, Micro-C, capture-C or HiChip data.
In summary, this version allows :
* Automatic detection and generation of annotation files based on igenomes
if not provided.
if not provided.
* Two-steps alignment of raw sequencing reads
* Reads filtering and detection of valid interaction products
* Generation of raw contact matrices for a set of resolutions
......
CITATIONS.md
+ 7
− 9
View file @ bee153c4
# nf-core/hic: Citations
## [HiC-Pro](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x)
> Servant N, Varoquaux N, Lajoie BR, Viara E, Chen C, Vert JP, Dekker J, Heard E, Barillot E. Genome Biology 2015, 16:259 doi: [10.1186/s13059-015-0831-x](https://dx.doi.org/10.1186/s13059-015-0831-x)
......@@ -15,27 +14,26 @@
## Pipeline tools
- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
## Software packaging/containerisation tools
- [Anaconda](https://anaconda.com)
* [Anaconda](https://anaconda.com)
> Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
> Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
> da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
README.md
+ 7
− 8
View file @ bee153c4
......@@ -23,11 +23,11 @@ On release, automated continuous integration tests run the pipeline on a full-si
## Pipeline summary
1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
2. Hi-C data processing
1. [`HiC-Pro`](https://github.com/nservant/HiC-Pro)
1. Mapping using a two steps strategy to rescue reads spanning the ligation
sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
sites ([`bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
2. Detection of valid interaction products
3. Duplicates removal
4. Generate raw and normalized contact maps ([`iced`](https://github.com/hiclib/iced))
......@@ -39,7 +39,6 @@ On release, automated continuous integration tests run the pipeline on a full-si
8. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooltools`](https://cooltools.readthedocs.io/en/latest/))
9. Quality control report ([`MultiQC`](https://multiqc.info/))
## Quick Start
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
......@@ -54,10 +53,10 @@ On release, automated continuous integration tests run the pipeline on a full-si
Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
> - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
> - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
> - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
> - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
> * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
> * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
> * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
> * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
4. Start running your own analysis!
......@@ -81,7 +80,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
## Citations
If you use nf-core/hic for your analysis, please cite it using the following doi: doi: [10.5281/zenodo.2669513](https://doi.org/10.5281/zenodo.2669513)
If you use nf-core/hic for your analysis, please cite it using the following doi: doi: [10.5281/zenodo.2669513](https://doi.org/10.5281/zenodo.2669513)
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
......
docs/output.md
+ 14
− 14
View file @ bee153c4
......@@ -20,9 +20,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
* [Compartments calling](#compartments-calling)
* [TADs calling](#tads-calling)
* [MultiQC](#multiqc) - aggregate report and quality controls, describing
results of the whole pipeline
results of the whole pipeline
* [Export](#exprot) - additionnal export for compatibility with downstream
analysis tool and visualization
analysis tool and visualization
## HiC-Pro
......@@ -79,14 +79,14 @@ reference genome and the digestion protocol.
Invalid pairs are classified as follow:
* Dangling end, i.e. unligated fragments (both reads mapped on the same
restriction fragment)
restriction fragment)
* Self circles, i.e. fragments ligated on themselves (both reads mapped on the
same restriction fragment in inverted orientation)
same restriction fragment in inverted orientation)
* Religation, i.e. ligation of juxtaposed fragments
* Filtered pairs, i.e. any pairs that do not match the filtering criteria on
inserts size, restriction fragments size
inserts size, restriction fragments size
* Dumped pairs, i.e. any pairs for which we were not able to reconstruct the
ligation product.
ligation product.
Only valid pairs involving two different restriction fragments are used to
build the contact maps.
......@@ -249,10 +249,10 @@ Usually, TADs results are presented as simple BED files, or bigWig files, with t
<details markdown="1">
<summary>Output files</summary>
- `multiqc/`
- `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
- `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
- `multiqc_plots/`: directory containing static images from the report in various formats.
* `multiqc/`
* `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
* `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
* `multiqc_plots/`: directory containing static images from the report in various formats.
</details>
......@@ -265,10 +265,10 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
<details markdown="1">
<summary>Output files</summary>
- `pipeline_info/`
- Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
- Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
- Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
* `pipeline_info/`
* Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
* Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
* Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
</details>
......
docs/usage.md
+ 22
− 22
View file @ bee153c4
......@@ -102,7 +102,7 @@ fails after three times then the pipeline is stopped.
## Core Nextflow arguments
> **NB:** These options are part of Nextflow and use a _single_ hyphen
(pipeline parameters use a double-hyphen).
> (pipeline parameters use a double-hyphen).
### `-profile`
......@@ -112,7 +112,7 @@ configuration presets for different compute environments.
Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io e.g [FastQC](https://quay.io/repository/biocontainers/fastqc) except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/).
> We highly recommend the use of Docker or Singularity containers for full
pipeline reproducibility, however when this is not possible, Conda is also supported.
> pipeline reproducibility, however when this is not possible, Conda is also supported.
The pipeline also dynamically loads configurations from
[https://github.com/nf-core/configs](https://github.com/nf-core/configs)
......@@ -131,21 +131,21 @@ If `-profile` is not specified, the pipeline will run locally and
expect all software to be
installed and available on the `PATH`. This is _not_ recommended.
- `docker`
- A generic configuration profile to be used with [Docker](https://docker.com/)
- `singularity`
- A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
- `podman`
- A generic configuration profile to be used with [Podman](https://podman.io/)
- `shifter`
- A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
- `charliecloud`
- A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
- `conda`
- A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
- `test`
- A profile with a complete configuration for automated testing
- Includes links to test data so needs no other parameters
* `docker`
* A generic configuration profile to be used with [Docker](https://docker.com/)
* `singularity`
* A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
* `podman`
* A generic configuration profile to be used with [Podman](https://podman.io/)
* `shifter`
* A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
* `charliecloud`
* A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
* `conda`
* A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
* `test`
* A profile with a complete configuration for automated testing
* Includes links to test data so needs no other parameters
### `-resume`
......@@ -224,7 +224,7 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
3. Create the custom config accordingly:
- For Docker:
* For Docker:
```nextflow
process {
......@@ -234,7 +234,7 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
}
```
- For Singularity:
* For Singularity:
```nextflow
process {
......@@ -244,7 +244,7 @@ The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementatio
}
```
- For Conda:
* For Conda:
```nextflow
process {
......@@ -330,7 +330,7 @@ Please note the following requirements:
1. The path must be enclosed in quotes
2. The path must have at least one `*` wildcard character
3. When using the pipeline with paired end data, the path must use `{1,2}`
notation to specify read pairs.
notation to specify read pairs.
If left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`
......@@ -467,7 +467,7 @@ Minimum mapping quality. Reads with lower quality are discarded. Default: 10
This parameter allows to automatically set the `--restriction_site` and
`--ligation_site` parameter according to the restriction enzyme you used.
Available keywords are 'hindiii', 'dpnii', 'mboi', 'arima'.
Available keywords are 'hindiii', 'dpnii', 'mboi', 'arima'.
```bash
--digestion 'hindiii'
......
modules.json
+ 1
− 1
View file @ bee153c4
......@@ -23,4 +23,4 @@
}
}
}
}
\ No newline at end of file
}
nextflow_schema.json
+ 67
− 39
View file @ bee153c4
......@@ -18,26 +18,31 @@
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/hic/usage#samplesheet-input).",
"description":
"Path to comma-separated file containing information about the samples in the experiment.",
"help_text":
"You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/hic/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"description":
"The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"help_text":
"Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"description":
"MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
......@@ -52,7 +57,8 @@
"type": "string",
"description": "Name of iGenomes reference.",
"fa_icon": "fas fa-book",
"help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
"help_text":
"If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
},
"fasta": {
"type": "string",
......@@ -60,7 +66,8 @@
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?s?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"help_text":
"This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"fa_icon": "far fa-file-code"
},
"igenomes_base": {
......@@ -76,11 +83,13 @@
"description": "Do not load the iGenomes reference config.",
"fa_icon": "fas fa-ban",
"hidden": true,
"help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
"help_text":
"Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
},
"bwt2_index": {
"type": "string",
"description": "Full path to directory containing Bowtie index including base name. i.e. `/path/to/index/base`.",
"description":
"Full path to directory containing Bowtie index including base name. i.e. `/path/to/index/base`.",
"fa_icon": "far fa-file-alt"
}
}
......@@ -94,36 +103,43 @@
"digestion": {
"type": "string",
"default": null,
"description": "Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)"
"description":
"Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)"
},
"restriction_site": {
"type": "string",
"default": null,
"description": "Restriction motifs used during digestion. Several motifs (comma separated) can be provided."
"description":
"Restriction motifs used during digestion. Several motifs (comma separated) can be provided."
},
"ligation_site": {
"type": "string",
"default": null,
"description": "Expected motif after DNA ligation. Several motifs (comma separated) can be provided."
"description":
"Expected motif after DNA ligation. Several motifs (comma separated) can be provided."
},
"chromosome_size": {
"type": "string",
"format": "file-path",
"description": "Full path to file specifying chromosome sizes (tab separated with chromosome name and size)`.",
"format": "file-path",
"description":
"Full path to file specifying chromosome sizes (tab separated with chromosome name and size)`.",
"fa_icon": "far fa-file-alt",
"help_text": "If not specified, the pipeline will build this file from the reference genome file"
},
"restriction_fragments": {
"type": "string",
"format": "file-path",
"format": "file-path",
"description": "Full path to restriction fragment (bed) file.",
"fa_icon": "far fa-file-alt",
"help_text": "This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --restriction_site option"
"help_text":
"This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --restriction_site option"
},
"save_reference": {
"type": "boolean",
"description": "If generated by the pipeline save the annotation and indexes in the results directory.",
"help_text": "Use this parameter to save all annotations to your results folder. These can then be used for future pipeline runs, reducing processing times.",
"description":
"If generated by the pipeline save the annotation and indexes in the results directory.",
"help_text":
"Use this parameter to save all annotations to your results folder. These can then be used for future pipeline runs, reducing processing times.",
"fa_icon": "fas fa-save"
}
}
......@@ -140,7 +156,8 @@
},
"min_cis_dist": {
"type": "integer",
"description": "Minimum distance between loci to consider. Useful for --dnase mode to remove spurious ligation products. Only values > 0 are considered"
"description":
"Minimum distance between loci to consider. Useful for --dnase mode to remove spurious ligation products. Only values > 0 are considered"
}
}
},
......@@ -217,12 +234,12 @@
"type": "boolean",
"description": "Save a BAM file where all reads are flagged by their interaction classes"
},
"save_pairs_intermediates": {
"save_pairs_intermediates": {
"type": "boolean",
"description": "Save all types of non valid read pairs in distinct output files"
}
}
},
},
"contact_maps": {
"title": "Contact maps",
"type": "object",
......@@ -264,10 +281,10 @@
"default": "5000",
"description": "Maximum resolution to build mcool file"
},
"save_raw_maps": {
"type": "boolean",
"description": "Save raw contact maps"
}
"save_raw_maps": {
"type": "boolean",
"description": "Save raw contact maps"
}
}
},
"downstream_analysis": {
......@@ -343,7 +360,8 @@
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"help_text":
"The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
......@@ -357,7 +375,8 @@
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"help_text":
"If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
......@@ -390,7 +409,8 @@
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"help_text":
"If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
......@@ -398,7 +418,8 @@
"default": 16,
"fa_icon": "fas fa-microchip",
"hidden": true,
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
"help_text":
"Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
......@@ -407,7 +428,8 @@
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
"help_text":
"Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
......@@ -416,7 +438,8 @@
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
"help_text":
"Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
......@@ -425,7 +448,8 @@
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"help_text":
"These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"help": {
"type": "boolean",
......@@ -437,7 +461,8 @@
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"help_text":
"The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
......@@ -447,7 +472,8 @@
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"help_text":
"An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
......@@ -495,11 +521,13 @@
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
"help_text":
"By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"enable_conda": {
"type": "boolean",
"description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
"description":
"Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
"hidden": true,
"fa_icon": "fas fa-bacon"
}
......@@ -536,8 +564,8 @@
},
{
"$ref": "#/definitions/generic_options"
},
{
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
......@@ -547,4 +575,4 @@
"$ref": "#/definitions/generic_options"
}
]
}
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment