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Fix redundant UDG flags #112

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merged 7 commits into from
Dec 17, 2018
Merged

Fix redundant UDG flags #112

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382d232
Fixing #89
apeltzer Dec 15, 2018
80f678d
Changelog to 112
apeltzer Dec 15, 2018
302105a
Parameter should match requirements
apeltzer Dec 15, 2018
dc9b067
Typo fix
apeltzer Dec 15, 2018
141f361
Help should be consistent too
apeltzer Dec 15, 2018
1e47950
Remove remains
apeltzer Dec 17, 2018
f91dba4
Cleaned up docs
apeltzer Dec 17, 2018
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Fixed`
* [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107)
* [#112](https://github.com/nf-core/eager/pull/112) - Remove [redundant UDG options](https://github.com/nf-core/eager/issues/89)

## [2.0.3] - 2018-12-09

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17 changes: 9 additions & 8 deletions docs/usage.md
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Expand Up @@ -265,14 +265,6 @@ This is by default set to `false`, but can be turned on to calculate on target m

Can be used to set a path to a BED file (3/6 column format) to calculate capture target efficiency on the fly. Will not be used without `--bedfile` set as parameter.

### `--udg` false

Defines whether Uracil-DNA glycosylase (UDG) treatment was used to repair DNA damage on the sequencing libraries. If set, the parameter is used by downstream tools such as PMDTools to estimate damage only on CpG sites that are left after such a treatment.

### `--udg_type "Half"`

If you have UDGhalf treated data (Rohland et al 2016), specify this parameter additionally to `--udg` to use a different model for DNA damage assessment in PMDTools.

## Step skipping parameters

Some of the steps in the pipeline can be executed optionally. If you specify specific steps to be skipped, there won't be any output related to these modules.
Expand Down Expand Up @@ -412,6 +404,15 @@ Specifies the length of the read start and end to be considered for profile gene

Specifies to run PMDTools for damage based read filtering and assessment of DNA damage in sequencing libraries. By default turned off.


### `--udg` false

Defines whether Uracil-DNA glycosylase (UDG) treatment was used to repair DNA damage on the sequencing libraries. If set, the parameter is used by downstream tools such as PMDTools to estimate damage only on CpG sites that are left after such a treatment.

### `--pmd_udg_type` \`half`

If you have UDGhalf treated data (Rohland et al 2016), specify `half` as option to this parameter to use a different model for DNA damage assessment in PMDTools. Specify the parameter with `full` and the DNA damage assesment will use CpG context only. If you don't specify the parameter at all, the library will be treated as non UDG treated.

### `--pmdtools_range`

Specifies the range in which to consider DNA damage from the ends of reads. By default set to `10`.
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8 changes: 3 additions & 5 deletions main.nf
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Expand Up @@ -34,8 +34,6 @@ def helpMessage() {

Input Data Additional Options:
--snpcapture Runs in SNPCapture mode (specify a BED file if you do this!)
--udg Specify that your libraries are treated with UDG
--udg_type Specify here if you have UDG half treated libraries, Set to 'Half' in that case

References If not specified in the configuration file or you wish to overwrite any of the references.
--bwa_index Path to BWA index
Expand Down Expand Up @@ -91,6 +89,7 @@ def helpMessage() {
--damageprofiler_length Specify length filter for DamageProfiler
--damageprofiler_threshold Specify number of bases to consider for damageProfiler
--run_pmdtools Turn on PMDtools
--udg_type Specify here if you have UDG half treated libraries, Set to 'half' in that case, or 'full' for UDG+. If not set, libraries are set to UDG-.
--pmdtools_range Specify range of bases for PMDTools
--pmdtools_threshold Specify PMDScore threshold for PMDTools
--pmdtools_reference_mask Specify a reference mask for PMDTools
Expand Down Expand Up @@ -139,8 +138,7 @@ params.bwa_index = false
params.seq_dict = false
params.fasta_index = false
params.saveReference = false
params.udg = false
params.udg_type = 'Half'
params.pmd_udg_type = 'half'

params.multiqc_config = "$baseDir/conf/multiqc_config.yaml"
params.email = false
Expand Down Expand Up @@ -936,7 +934,7 @@ process pmdtools {

script:
//Check which treatment for the libraries was used
def treatment = params.udg ? (params.udg_type =='half' ? '--UDGhalf' : '--CpG') : '--UDGminus'
def treatment = params.pmd_udg_type ? (params.pmd_udg_type =='half' ? '--UDGhalf' : '--CpG') : '--UDGminus'
if(params.snpcapture){
snpcap = (params.pmdtools_reference_mask != '') ? "--refseq ${params.pmdtools_reference_mask}" : ''
log.info"######No reference mask specified for PMDtools, therefore ignoring that for downstream analysis!"
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