From 382d2325eea9e5919833341beb59297732a481c2 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sun, 16 Dec 2018 00:42:37 +0100 Subject: [PATCH 1/7] Fixing #89 --- CHANGELOG.md | 1 + docs/usage.md | 6 ++++-- main.nf | 5 ++--- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cb016e5e7..cfcb1927c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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) +* [#111](https://github.com/nf-core/eager/pull/111) - Remove [redundant UDG options](https://github.com/nf-core/eager/issues/89) ## [2.0.3] - 2018-12-09 diff --git a/docs/usage.md b/docs/usage.md index 8a90a3a25..7a1f93f87 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -269,9 +269,11 @@ Can be used to set a path to a BED file (3/6 column format) to calculate capture 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"` +### `--pmd_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. +half' ? '--UDGhalf' : '--CpG') : '--UDGminus' + +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 UDG-. ## Step skipping parameters diff --git a/main.nf b/main.nf index 8899fea60..94eb59e72 100644 --- a/main.nf +++ b/main.nf @@ -139,8 +139,7 @@ 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 @@ -936,7 +935,7 @@ 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 ${params.pmdtools_reference_mask}" : '' log.info"######No reference mask specified for PMDtools, therefore ignoring that for downstream analysis!" From 80f678d026fdcf9faac9d5cb601de97ea9405707 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sun, 16 Dec 2018 00:44:18 +0100 Subject: [PATCH 2/7] Changelog to 112 --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cfcb1927c..5405ae64b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` * [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107) -* [#111](https://github.com/nf-core/eager/pull/111) - Remove [redundant UDG options](https://github.com/nf-core/eager/issues/89) +* [#112](https://github.com/nf-core/eager/pull/112) - Remove [redundant UDG options](https://github.com/nf-core/eager/issues/89) ## [2.0.3] - 2018-12-09 From 302105a06205cc24404e608020ff9d9ee26bf3d0 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sun, 16 Dec 2018 00:45:04 +0100 Subject: [PATCH 3/7] Parameter should match requirements --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 94eb59e72..3f3bf88f6 100644 --- a/main.nf +++ b/main.nf @@ -139,7 +139,7 @@ params.bwa_index = false params.seq_dict = false params.fasta_index = false params.saveReference = false -params.pmd_udg_type = 'Half' +params.pmd_udg_type = 'half' params.multiqc_config = "$baseDir/conf/multiqc_config.yaml" params.email = false From dc9b0672762b21935a96fc77e84e41f58f0ba40c Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sun, 16 Dec 2018 00:54:40 +0100 Subject: [PATCH 4/7] Typo fix --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 3f3bf88f6..874532db4 100644 --- a/main.nf +++ b/main.nf @@ -935,7 +935,7 @@ process pmdtools { script: //Check which treatment for the libraries was used - def treatment = params.pmd_udg_type ?: (params.pmd_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!" From 141f361504cd3b3ce7de45cb97d932abbe94316b Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sun, 16 Dec 2018 00:57:16 +0100 Subject: [PATCH 5/7] Help should be consistent too --- main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 874532db4..af140c3e8 100644 --- a/main.nf +++ b/main.nf @@ -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 @@ -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 From 1e47950988b2763700641817803dbf3f5a0b053a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 17 Dec 2018 13:40:52 +0100 Subject: [PATCH 6/7] Remove remains --- docs/usage.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 7a1f93f87..5e5dc2787 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -271,8 +271,6 @@ Defines whether Uracil-DNA glycosylase (UDG) treatment was used to repair DNA da ### `--pmd_udg_type` \`half` -half' ? '--UDGhalf' : '--CpG') : '--UDGminus' - 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 UDG-. ## Step skipping parameters From f91dba4ddbf27adc2fc6652f523c1c718c854651 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 17 Dec 2018 13:43:17 +0100 Subject: [PATCH 7/7] Cleaned up docs --- docs/usage.md | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 5e5dc2787..4edc9af16 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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. - -### `--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 UDG-. - ## 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. @@ -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`.