From f82ec62213eaadedd19241af8ea5dc4120baf26f Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Sat, 7 May 2022 23:28:31 +0200
Subject: [PATCH] [MODIF] prettier
---
CHANGELOG.md | 142 ++++++++++++++++++++++++------------------------
CITATIONS.md | 14 ++---
README.md | 8 +--
docs/output.md | 98 ++++++++++++++++-----------------
docs/usage.md | 44 +++++++--------
environment.yml | 6 +-
6 files changed, 156 insertions(+), 156 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0418c64..3478c9d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,122 +7,122 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`
-* DSL2 version of nf-core-hic pipeline
+- DSL2 version of nf-core-hic pipeline
## v1.3.1 - 2021-09-25
### `Fixed`
-* Fix bug in conda environment for cooltools (#109)
+- Fix bug in conda environment for cooltools (#109)
## v1.3.0 - 2021-05-22
-* Change the `/tmp/` folder to `./tmp/` folder so that all tmp files are now in the work directory (#24)
-* Add `--hicpro_maps` options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler
-* Add chromosome compartments calling with cooltools (#53)
-* Add HiCExplorer distance decay quality control (#54)
-* Add HiCExplorer TADs calling (#55)
-* Add insulation score TADs calling (#55)
-* Generate cooler/txt contact maps
-* Normalize Hi-C data with cooler instead of iced
-* New `--digestion` parameter to automatically set the restriction_site and ligation_site motifs
-* New `--keep_multi` and `keep_dup` options. Default: false
-* Template update for nf-core/tools
-* Minor fix to summary log messages in pipeline header
+- Change the `/tmp/` folder to `./tmp/` folder so that all tmp files are now in the work directory (#24)
+- Add `--hicpro_maps` options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler
+- Add chromosome compartments calling with cooltools (#53)
+- Add HiCExplorer distance decay quality control (#54)
+- Add HiCExplorer TADs calling (#55)
+- Add insulation score TADs calling (#55)
+- Generate cooler/txt contact maps
+- Normalize Hi-C data with cooler instead of iced
+- New `--digestion` parameter to automatically set the restriction_site and ligation_site motifs
+- New `--keep_multi` and `keep_dup` options. Default: false
+- Template update for nf-core/tools
+- Minor fix to summary log messages in pipeline header
### `Fixed`
-* Fix bug in stats report which were not all correcly exported in the results folder
-* Fix recurrent bug in input file extension (#86)
-* Fix bug in `--bin_size` parameter (#85)
-* `--min_mapq` is ignored if `--keep_multi` is used
+- Fix bug in stats report which were not all correcly exported in the results folder
+- Fix recurrent bug in input file extension (#86)
+- Fix bug in `--bin_size` parameter (#85)
+- `--min_mapq` is ignored if `--keep_multi` is used
### `Deprecated`
-* `--rm_dup` and `--rm_multi` are replaced by `--keep_dups` and `--keep_multi`
+- `--rm_dup` and `--rm_multi` are replaced by `--keep_dups` and `--keep_multi`
## v1.2.2 - 2020-09-02
### `Added`
-* Template update for nf-core/tools v1.10.2
-* Add the `--fastq_chunks_size` to specify the number of reads per chunks if split_fastq is true
+- Template update for nf-core/tools v1.10.2
+- Add the `--fastq_chunks_size` to specify the number of reads per chunks if split_fastq is true
### `Fixed`
-* Bug in `--split_fastq` option not recognized
+- Bug in `--split_fastq` option not recognized
## v1.2.1 - 2020-07-06
### `Fixed`
-* Fix issue with `--fasta` option and `.fa` extension (#66)
+- Fix issue with `--fasta` option and `.fa` extension (#66)
## v1.2.0 - 2020-06-18
### `Added`
-* Bump v1.2.0
-* Merge template nf-core 1.9
-* Move some options to camel_case
-* Update python scripts for python3
-* Update conda environment file
- * python base `2.7.15` > `3.7.6`
- * pip `19.1` > `20.0.1`
- * scipy `1.2.1` > `1.4.1`
- * numpy `1.16.3` > `1.18.1`
- * bx-python `0.8.2` > `0.8.8`
- * pysam `0.15.2` > `0.15.4`
- * 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
+- Bump v1.2.0
+- Merge template nf-core 1.9
+- Move some options to camel_case
+- Update python scripts for python3
+- Update conda environment file
+ - python base `2.7.15` > `3.7.6`
+ - pip `19.1` > `20.0.1`
+ - scipy `1.2.1` > `1.4.1`
+ - numpy `1.16.3` > `1.18.1`
+ - bx-python `0.8.2` > `0.8.8`
+ - pysam `0.15.2` > `0.15.4`
+ - 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
### `Fixed`
-* Fix error in doc for Arima kit usage
-* Sort output of `get_valid_interaction` process as the input files of `remove_duplicates`
+- 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)
### `Deprecated`
-* Command line options converted to `camel_case`:
- * `--skipMaps` > `--skip_maps`
- * `--skipIce` > `--skip_ice`
- * `--skipCool` > `--skip_cool`
- * `--skipMultiQC` > `--skip_multiqc`
- * `--saveReference` > `--save_reference`
- * `--saveAlignedIntermediates` > `--save_aligned_intermediates`
- * `--saveInteractionBAM` > `--save_interaction_bam`
+- Command line options converted to `camel_case`:
+ - `--skipMaps` > `--skip_maps`
+ - `--skipIce` > `--skip_ice`
+ - `--skipCool` > `--skip_cool`
+ - `--skipMultiQC` > `--skip_multiqc`
+ - `--saveReference` > `--save_reference`
+ - `--saveAlignedIntermediates` > `--save_aligned_intermediates`
+ - `--saveInteractionBAM` > `--save_interaction_bam`
## v1.1.1 - 2020-04-02
### `Fixed`
-* Fix bug in tag. Remove '['
+- Fix bug in tag. Remove '['
## v1.1.0 - 2019-10-15
### `Added`
-* Update hicpro2higlass with `-p` parameter
-* Support 'N' base motif in restriction/ligation sites
-* Support multiple restriction enzymes/ligattion sites (comma separated) ([#31](https://github.com/nf-core/hic/issues/31))
-* Add --saveInteractionBAM option
-* Add DOI ([#29](https://github.com/nf-core/hic/issues/29))
-* Update manual ([#28](https://github.com/nf-core/hic/issues/28))
+- Update hicpro2higlass with `-p` parameter
+- Support 'N' base motif in restriction/ligation sites
+- Support multiple restriction enzymes/ligattion sites (comma separated) ([#31](https://github.com/nf-core/hic/issues/31))
+- Add --saveInteractionBAM option
+- Add DOI ([#29](https://github.com/nf-core/hic/issues/29))
+- Update manual ([#28](https://github.com/nf-core/hic/issues/28))
### `Fixed`
-* Fix bug for reads extension `_1`/`_2` ([#30](https://github.com/nf-core/hic/issues/30))
+- Fix bug for reads extension `_1`/`_2` ([#30](https://github.com/nf-core/hic/issues/30))
## v1.0 - [2019-05-06]
@@ -138,11 +138,11 @@ 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
+- Automatic detection and generation of annotation files based on igenomes
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
-* Normalization of the contact maps using the ICE algorithm
-* Generation of cooler file for visualization on [higlass](https://higlass.io/)
-* Quality report based on HiC-Pro MultiQC module
+- 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
+- Normalization of the contact maps using the ICE algorithm
+- Generation of cooler file for visualization on [higlass](https://higlass.io/)
+- Quality report based on HiC-Pro MultiQC module
diff --git a/CITATIONS.md b/CITATIONS.md
index 5859810..0313a1a 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -14,26 +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.
diff --git a/README.md b/README.md
index 37b9d3e..8e7f9b9 100644
--- a/README.md
+++ b/README.md
@@ -53,10 +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!
diff --git a/docs/output.md b/docs/output.md
index bb116f8..f93382f 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -9,19 +9,19 @@ The directories listed below will be created in the results directory after the
The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
-* [HiC-Pro](#hicpro)
- * [Reads alignment](#reads-alignment)
- * [Valid pairs detection](#valid-pairs-detection)
- * [Duplicates removal](#duplicates-removal)
- * [Contact maps](#hicpro-contact-maps)
-* [Hi-C contact maps](#hic-contact-maps)
-* [Downstream analysis](#downstream-analysis)
- * [Distance decay](#distance-decay)
- * [Compartments calling](#compartments-calling)
- * [TADs calling](#tads-calling)
-* [MultiQC](#multiqc) - aggregate report and quality controls, describing
+- [HiC-Pro](#hicpro)
+ - [Reads alignment](#reads-alignment)
+ - [Valid pairs detection](#valid-pairs-detection)
+ - [Duplicates removal](#duplicates-removal)
+ - [Contact maps](#hicpro-contact-maps)
+- [Hi-C contact maps](#hic-contact-maps)
+- [Downstream analysis](#downstream-analysis)
+ - [Distance decay](#distance-decay)
+ - [Compartments calling](#compartments-calling)
+ - [TADs calling](#tads-calling)
+- [MultiQC](#multiqc) - aggregate report and quality controls, describing
results of the whole pipeline
-* [Export](#exprot) - additionnal export for compatibility with downstream
+- [Export](#exprot) - additionnal export for compatibility with downstream
analysis tool and visualization
## HiC-Pro
@@ -48,18 +48,18 @@ mapping step.
**Output directory: `results/hicpro/mapping`**
-* `*bwt2pairs.bam` - final BAM file with aligned paired data
-* `*.pairstat` - mapping statistics
+- `*bwt2pairs.bam` - final BAM file with aligned paired data
+- `*.pairstat` - mapping statistics
if `--saveAlignedIntermediates` is specified, additional mapping file results
are available ;
-* `*.bam` - Aligned reads (R1 and R2) from end-to-end alignment
-* `*_unmap.fastq` - Unmapped reads after end-to-end alignment
-* `*_trimmed.fastq` - Trimmed reads after end-to-end alignment
-* `*_trimmed.bam` - Alignment of trimmed reads
-* `*bwt2merged.bam` - merged BAM file after the two-steps alignment
-* `*.mapstat` - mapping statistics per read mate
+- `*.bam` - Aligned reads (R1 and R2) from end-to-end alignment
+- `*_unmap.fastq` - Unmapped reads after end-to-end alignment
+- `*_trimmed.fastq` - Trimmed reads after end-to-end alignment
+- `*_trimmed.bam` - Alignment of trimmed reads
+- `*bwt2merged.bam` - merged BAM file after the two-steps alignment
+- `*.mapstat` - mapping statistics per read mate
Usually, a high fraction of reads is expected to be aligned on the genome
(80-90%). Among them, we usually observed a few percent (around 10%) of step 2
@@ -78,14 +78,14 @@ reference genome and the digestion protocol.
Invalid pairs are classified as follow:
-* Dangling end, i.e. unligated fragments (both reads mapped on the same
+- Dangling end, i.e. unligated fragments (both reads mapped on the same
restriction fragment)
-* Self circles, i.e. fragments ligated on themselves (both reads mapped on the
+- Self circles, i.e. fragments ligated on themselves (both reads mapped on the
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
+- 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
-* Dumped pairs, i.e. any pairs for which we were not able to reconstruct the
+- Dumped pairs, i.e. any pairs for which we were not able to reconstruct the
ligation product.
Only valid pairs involving two different restriction fragments are used to
@@ -101,12 +101,12 @@ can thus be discarded using the `--min_cis_dist` parameter.
**Output directory: `results/hicpro/valid_pairs`**
-* `*.validPairs` - List of valid ligation products
-* `*.DEpairs` - List of dangling-end products
-* `*.SCPairs` - List of self-circle products
-* `*.REPairs` - List of religation products
-* `*.FiltPairs` - List of filtered pairs
-* `*RSstat` - Statitics of number of read pairs falling in each category
+- `*.validPairs` - List of valid ligation products
+- `*.DEpairs` - List of dangling-end products
+- `*.SCPairs` - List of self-circle products
+- `*.REPairs` - List of religation products
+- `*.FiltPairs` - List of filtered pairs
+- `*RSstat` - Statitics of number of read pairs falling in each category
The validPairs are stored using a simple tab-delimited text format ;
@@ -135,8 +135,8 @@ removed if the `--rm_dup` parameter is used.
**Output directory: `results/hicpro/valid_pairs`**
-* `*allValidPairs` - combined valid pairs from all read chunks
-* `*mergestat` - statistics about duplicates removal and valid pairs information
+- `*allValidPairs` - combined valid pairs from all read chunks
+- `*mergestat` - statistics about duplicates removal and valid pairs information
Additional quality controls such as fragment size distribution can be extracted
from the list of valid interaction products.
@@ -166,15 +166,15 @@ is specified on the command line.
**Output directory: `results/hicpro/matrix`**
-* `*.matrix` - genome-wide contact maps
-* `*_iced.matrix` - genome-wide iced contact maps
+- `*.matrix` - genome-wide contact maps
+- `*_iced.matrix` - genome-wide iced contact maps
The contact maps are generated for all specified resolutions
(see `--bin_size` argument).
A contact map is defined by :
-* A list of genomic intervals related to the specified resolution (BED format).
-* A matrix, stored as standard triplet sparse format (i.e. list format).
+- A list of genomic intervals related to the specified resolution (BED format).
+- A matrix, stored as standard triplet sparse format (i.e. list format).
Based on the observation that a contact map is symmetric and usually sparse,
only non-zero values are stored for half of the matrix. The user can specified
@@ -227,8 +227,8 @@ Here, we use the implementation available in the [`cooltools`](https://cooltools
Results are available in **`results/compartments/`** folder and includes :
-* `*cis.vecs.tsv`: eigenvectors decomposition along the genome
-* `*cis.lam.txt`: eigenvalues associated with the eigenvectors
+- `*cis.vecs.tsv`: eigenvectors decomposition along the genome
+- `*cis.lam.txt`: eigenvalues associated with the eigenvectors
### TADs calling
@@ -239,8 +239,8 @@ TADs calling remains a challenging task, and even if many methods have been prop
Currently, the pipeline proposes two approaches :
-* Insulation score using the [`cooltools`](https://cooltools.readthedocs.io/en/latest/cli.html#cooltools-diamond-insulation) package. Results are availabe in **`results/tads/insulation`**.
-* [`HiCExplorer TADs calling`](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html). Results are available at **`results/tads/hicexplorer`**.
+- Insulation score using the [`cooltools`](https://cooltools.readthedocs.io/en/latest/cli.html#cooltools-diamond-insulation) package. Results are availabe in **`results/tads/insulation`**.
+- [`HiCExplorer TADs calling`](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html). Results are available at **`results/tads/hicexplorer`**.
Usually, TADs results are presented as simple BED files, or bigWig files, with the position of boundaries along the genome.
@@ -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>
diff --git a/docs/usage.md b/docs/usage.md
index 695cc1c..885a5ca 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -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 {
@@ -483,10 +483,10 @@ The precise cutting site of the restriction enzyme has to be specified using
the '^' character. Default: 'A^AGCTT'
Here are a few examples:
-* MboI: ^GATC
-* DpnII: ^GATC
-* HindIII: A^AGCTT
-* ARIMA kit: ^GATC,G^ANTC
+- MboI: ^GATC
+- DpnII: ^GATC
+- HindIII: A^AGCTT
+- ARIMA kit: ^GATC,G^ANTC
Note that multiples restriction motifs can be provided (comma-separated) and
that 'N' base are supported.
diff --git a/environment.yml b/environment.yml
index dabfb9d..50e0fa7 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,7 +8,7 @@ channels:
dependencies:
- conda-forge::python=3.9.12=h9a8a25e_1_cpython
- pip=22.0.4=pyhd8ed1ab_0
- - conda-forge::tbb=2020.2=hc9558a2_0
+ - conda-forge::tbb=2020.2=hc9558a2_0
- conda-forge::scipy=1.8.0=py39hee8e79c_1
- conda-forge::numpy=1.22.3=py39hc58783e_2
- bioconda::iced=0.5.10=py39h919a90d_1
@@ -22,11 +22,11 @@ dependencies:
- bioconda::multiqc=1.12=pyhdfd78af_0
- bioconda::fastqc=0.11.9=hdfd78af_1
-## Dev tools
+ ## Dev tools
- bioconda::hicexplorer=3.7.2=pyhdfd78af_1
- bioconda::bioconductor-hitc=1.38.0=r41hdfd78af_0
- conda-forge::r-optparse=1.7.1=r41hc72bb7e_0
- bioconda::ucsc-bedgraphtobigwig=377=ha8a8165_3
- conda-forge::cython=0.29.28=py39h5a03fae_2
- pip:
- - fanc==0.9.23
\ No newline at end of file
+ - fanc==0.9.23
--
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