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Verified Commit de26b8fa authored by Mia Croiset's avatar Mia Croiset
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update usage readme with saving options

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# nf-core/hic: Documentation
# Meta HiC pipeline: Documentation
The nf-core/hic documentation is split into the following pages:
The Meta HiC pipeline is split into the following pages:
- [Usage](usage.md)
- An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
- [Usage hicpro workflow](usage.md)
- An overview of how the pipeline works, how to run it and a description of all of the different command-line flags for the hicpro workflow.
- [Usage hicstuff workflow](hicstuff_usage.md)
- An overview of how the pipeline works, how to run it and a description of all of the different command-line flags for the hicstuff workflow.
- [Output](output.md)
- An overview of the different results produced by the pipeline and how to interpret them.
- /!\TO UPDATE/!\ An overview of the different results produced by the pipeline and how to interpret them.
You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)
......@@ -124,6 +124,14 @@ Default: '--very-sensitive-local'
--hicstuff_bwt2_align_opts '[Options for bowtie2 mapping on full reads]'
```
#### `--save_bam`
If specified, save BAM files after mapping. Default: false
```bash
--save_bam
```
### Fragment enzyme
#### `--hicstuff_min_size`
......@@ -168,6 +176,14 @@ Name of fragments plot file. Default: 'frags_hist.pdf'
--hicstuff_frags_plot_path '[Name of fragments plot file]'
```
#### `--save_fragments`
If specified, save fragments file. Default: false
```bash
--save_fragments
```
### Bam2pairs
#### `--hicstuff_valid_pairs`
......@@ -193,6 +209,15 @@ Minimum mapping quality required to keep a pair of Hi-C reads. Default:30
[#### `--hicstuff_circular`](#hicstuff_circular)
#### `--save_pairs`
If specified, save pair files. Default: false
```bash
--save_pairs
```
### Matrix
#### `--hicstuff_matrix`
......@@ -324,3 +349,11 @@ If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If
--filter_pcr_picard
```
#### `--save_bam_intermediates`
If specified, save BAM files after PICARD pcr filtering. Default: false
```bash
--save_bam_intermediates
```
......@@ -400,6 +400,22 @@ Note that in this case the `--min_mapq` parameter is ignored.
--keep_multi
```
#### `--save_bam_intermediates`
If specified, save BAM files after PICARD pcr filtering. Default: false
```bash
--save_bam_intermediates
```
#### `--save_pairs`
If specified, save pair files. Default: false
```bash
--save_pairs
```
## Genome-wide contact maps
Once the list of valid pairs is available, the standard is now to move on the `cooler`
......@@ -555,6 +571,14 @@ results folder. Default: false
--save_aligned_inermediates
```
### `--save_bam`
If specified, save BAM files after mapping. Default: false
```bash
--save_bam
```
### `--save_interaction_bam`
If specified, write a BAM file with all classified reads (valid pairs,
......
......@@ -231,7 +231,7 @@
},
"save_bam_intermediates": {
"type": "boolean",
"description": "Save BAM files PICARD pcr duplicates filtering"
"description": "Save BAM files PICARD pcr duplicates filtering"
},
"save_pairs": {
"type": "boolean",
......
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