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Commit 2a24e909 authored by nservant's avatar nservant
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[LINT] fix linting issues

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......@@ -9,20 +9,20 @@ 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:
- [From raw data to valid pairs](#from-raw-data-to-valid-pairs)
- [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
* [From raw data to valid pairs](#from-raw-data-to-valid-pairs)
* [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
## From raw data to valid pairs
......@@ -50,17 +50,17 @@ mapping step.
**Output directory: `results/hicpro/mapping`**
- `*bwt2pairs.bam` - final BAM file with aligned paired data
* `*bwt2pairs.bam` - final BAM file with aligned paired data
if `--save_aligned_intermediates` 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
......@@ -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
* 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
......@@ -102,12 +102,12 @@ 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
Of note, these results are saved only if `--save_pairs_intermediates` is used.
The `validPairs` are stored using a simple tab-delimited text format ;
......@@ -138,7 +138,7 @@ removed (see `--keep_dups` to disable duplicates filtering).
**Output directory: `results/hicpro/valid_pairs`**
- `*allValidPairs` - combined valid pairs from all read chunks
* `*allValidPairs` - combined valid pairs from all read chunks
Additional quality controls such as fragment size distribution can be extracted
from the list of valid interaction products.
......@@ -160,7 +160,7 @@ detection of valid pairs.
**Output directory: `results/hicpro/valid_pairs/pairix`**
- `*pairix` - compressed and indexed pairs file
* `*pairix` - compressed and indexed pairs file
#### Statistics
......@@ -169,10 +169,10 @@ All results are available in `results/hicpro/stats`.
**Output directory: `results/hicpro/stats`**
- *mapstat - mapping statistics per read mate
- *pairstat - R1/R2 pairing statistics
- *RSstat - Statitics of number of read pairs falling in each category
- *mergestat - statistics about duplicates removal and valid pairs information
* \*mapstat - mapping statistics per read mate
* \*pairstat - R1/R2 pairing statistics
* \*RSstat - Statitics of number of read pairs falling in each category
* \*mergestat - statistics about duplicates removal and valid pairs information
#### Contact maps
......@@ -192,15 +192,15 @@ 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
......@@ -254,8 +254,8 @@ 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
......@@ -266,8 +266,8 @@ 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.
......@@ -276,10 +276,10 @@ 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>
......@@ -292,10 +292,10 @@ 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>
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