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Verified Commit c64b19ad authored by Mia Croiset's avatar Mia Croiset
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correct param name in usage docs

parent ce06ca06
Branches nf-core-template-merge-2.3.1
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......@@ -301,13 +301,13 @@ Name of distance law table plot if hicstuff_distance_plot is true. Default: dist
--hicstuff_distance_out_plot '[Name of distance law plot file]'
```
#### `--filter_pcr`
#### `--hicstuff_filter_pcr`
If true, PCR duplicates will be filtered based on genomic positions Pairs where both reads have exactly the same coordinates are considered duplicates and only one of those will be conserved. Default: false
```bash
--hicstuff_filter_pcr
```
> :warning: **Warning**: if true, `--filter_pcr_duplicates` **must** be false
> :warning: **Warning**: if true, `--filter_pcr_picard` **must** be false
#### `--hicstuff_filter_pcr_out_file`
Name of pair file after PCR filtering. Default: 'valid_idx_pcrfree.pairs'
......@@ -316,11 +316,11 @@ Name of pair file after PCR filtering. Default: 'valid_idx_pcrfree.pairs'
--hicstuff_filter_pcr_out_file '[Name of pcr free pair file]'
```
#### `--filter_pcr_duplicates`
#### `--filter_pcr_picard`
If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--keep_dups` **must** also be true. Default:'false'
If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--hicstuff_filter_pcr` **must** be false. Default:'false'
```bash
--filter_pcr_duplicates
--filter_pcr_picard
```
......@@ -381,16 +381,14 @@ If specified, duplicate reads are not discarded before building contact maps.
--keep_dups
```
#### `--filter_pcr_duplicates`
#### `--filter_pcr_picard`
If specified, duplicate reads are filtered using PICARD MarkDuplicate method. If true, `--keep_dups` **must** also be true. Default:'false'
```bash
--filter_pcr_duplicates
--filter_pcr_picard
```
> :warning: **Warning**: this option is **not** functional yet with the workflow hicpro. Setting this parameter true will fail your run.
#### `--keep_multi`
If specified, reads that aligned multiple times on the genome are not discarded.
......
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