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Add shiftfasta #354

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merged 9 commits into from
May 29, 2023
Merged

Add shiftfasta #354

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f6afe61
add module and remove redundant parameters
ramprasadn May 25, 2023
921040f
Merge branch 'devplaceholder' of github.com:nf-core/raredisease into …
ramprasadn May 26, 2023
49dd613
update configs
ramprasadn May 26, 2023
fd79ab7
update input channel definitions
ramprasadn May 26, 2023
743c35b
update docs
ramprasadn May 26, 2023
f0f866d
update changelog
ramprasadn May 26, 2023
c0a869e
fix lint
ramprasadn May 26, 2023
4b6b9ea
update conf
ramprasadn May 27, 2023
48af7d5
update faidx
ramprasadn May 29, 2023
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7 changes: 7 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,13 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v2.0.0 - []

### `Added`

- GATK's ShiftFasta to generate all the files required for mitochondrial analysis
- Feature to calculate CADD scores for indels

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## v1.0.0 - [2023-03-31]

Initial release of nf-core/raredisease, created with the [nf-core](https://nf-co.re/) template.
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14 changes: 4 additions & 10 deletions conf/modules/align_and_call_MT.config
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Expand Up @@ -16,18 +16,15 @@
//

process {
withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:.*' {
ext.when = { params.mt_fasta_shift && params.mt_intervals && !(params.analysis_type == "wes") }
}

withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:BWAMEM2_MEM_MT' {
ext.when = { params.mt_fasta_shift && params.mt_intervals && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
}

withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:SENTIEON_BWAMEM_MT' {
ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
ext.when = { params.mt_fasta_shift && params.mt_intervals && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
ext.prefix = { "${meta.id}.sorted" }
}

Expand Down Expand Up @@ -69,18 +66,15 @@ process {
//

process {
withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:.*' {
ext.when = { params.mt_fasta_shift && params.mt_intervals_shift && !(params.analysis_type == "wes") }
}

withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:BWAMEM2_MEM_MT' {
ext.when = { params.mt_fasta_shift && params.mt_intervals_shift && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
}

withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:SENTIEON_BWAMEM_MT' {
ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
ext.when = { params.mt_fasta_shift && params.mt_intervals_shift && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
ext.prefix = { "${meta.id}.sorted" }
}

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2 changes: 1 addition & 1 deletion conf/modules/analyse_MT.config
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Expand Up @@ -17,6 +17,7 @@

process {
withName: '.*ANALYSE_MT:.*' {
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") }
publishDir = [
enabled: false
]
Expand All @@ -25,7 +26,6 @@ process {

process {
withName: '.*ANALYSE_MT:PICARD_LIFTOVERVCF' {
ext.when = { params.mt_fasta_shift && params.mt_intervals_shift && !(params.analysis_type == "wes") }
ext.prefix = { "${meta.id}_liftover" }
}
}
3 changes: 0 additions & 3 deletions conf/modules/convert_mt_bam_to_fastq.config
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Expand Up @@ -16,9 +16,6 @@
//

process {
withName: '.*ANALYSE_MT:CONVERT_MT_BAM_TO_FASTQ:.*' {
ext.when = { params.mt_fasta_shift && !(params.analysis_type == "wes") }
}

withName: '.*ANALYSE_MT:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT' {
beforeScript = {"mkdir ./tmp"}
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3 changes: 0 additions & 3 deletions conf/modules/merge_annotate_MT.config
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Expand Up @@ -16,9 +16,6 @@
//

process {
withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:.*' {
ext.when = { params.mt_fasta_shift && params.mt_intervals && !(params.analysis_type == "wes") }
}

withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:GATK4_MERGEVCFS_LIFT_UNLIFT_MT' {
ext.prefix = { "${meta.id}_merged" }
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25 changes: 17 additions & 8 deletions conf/modules/prepare_references.config
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Expand Up @@ -29,16 +29,16 @@ process {
ext.when = {!params.bwamem2 && params.aligner == "bwamem2"}
}

withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_SHIFT_MT' {
ext.when = {!params.mt_bwamem2_index_shift && params.mt_fasta_shift && !(params.analysis_type == "wes") && params.aligner == "bwamem2"}
withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT' {
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "bwamem2"}
}

withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_GENOME' {
ext.when = {!params.bwa && params.aligner == "sentieon"}
}

withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_SHIFT_MT' {
ext.when = {!params.mt_bwa_index_shift && params.mt_fasta_shift && !(params.analysis_type == "wes") && params.aligner == "sentieon"}
withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT_SHIFT' {
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "sentieon"}
}

withName: '.*PREPARE_REFERENCES:BWA_INDEX_GENOME' {
Expand All @@ -49,16 +49,25 @@ process {
ext.when = {!params.fai}
}

withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_SHIFT_MT' {
ext.when = {!params.mt_fai_shift && params.mt_fasta_shift && !(params.analysis_type == "wes")}
withName: '.*PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT' {
ext.args = { " ${params.mito_name} -o ${meta.id}_mt.fa" }
ext.when = {!params.mt_fasta && !params.skip_mt_analysis}
}

withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT_SHIFT' {
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes")}
}

withName: '.*PREPARE_REFERENCES:GATK_SD' {
ext.when = {!params.sequence_dictionary}
}

withName: '.*PREPARE_REFERENCES:GATK_SD_SHIFT_MT' {
ext.when = {!params.mt_sequence_dictionary_shift && params.mt_fasta_shift && !(params.analysis_type == "wes")}
withName: '.*PREPARE_REFERENCES:GATK_SHIFTFASTA' {
ext.args = { "--interval-file-name ${meta.id}_mt" }
}

withName: '.*PREPARE_REFERENCES:GATK_SD_MT_SHIFT' {
ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes")}
}

withName: '.*PREPARE_REFERENCES:GET_CHROM_SIZES' {
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4 changes: 0 additions & 4 deletions conf/test.config
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Expand Up @@ -34,10 +34,6 @@ params {
intervals_y = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list"
known_dbsnp = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
ml_model = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
mt_fasta_shift = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.fa"
mt_intervals = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt.intervals"
mt_intervals_shift = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.intervals"
mt_backchain_shift = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.back_chain"
reduced_penetrance = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"
score_config_snv = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
score_config_sv = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini"
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4 changes: 0 additions & 4 deletions conf/test_one_sample.config
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Expand Up @@ -34,10 +34,6 @@ params {
intervals_y = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list"
known_dbsnp = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
ml_model = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
mt_fasta_shift = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.fa"
mt_intervals = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt.intervals"
mt_intervals_shift = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.intervals"
mt_backchain_shift = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.back_chain"
reduced_penetrance = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"
score_config_snv = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
score_config_sv = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini"
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22 changes: 8 additions & 14 deletions docs/usage.md
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Expand Up @@ -219,20 +219,14 @@ The mandatory and optional parameters for each category are tabulated below.

##### 8. Mitochondrial analysis

| Mandatory | Optional |
| ------------------------------ | -------- |
| genome | |
| mt_backchain_shift<sup>1</sup> | |
| mito_name | |
| mt_fasta_shift | |
| mt_intervals | |
| mt_intervals_shift | |
| vcfanno_resources | |
| vcfanno_toml | |
| vep_cache_version | |
| vep_cache | |

<sup>1</sup>Can be generated by GATK's [ShiftFasta](https://gatk.broadinstitute.org/hc/en-us/articles/9570501436827-ShiftFasta-BETA-). Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/mt_shift8000.back_chain).
| Mandatory | Optional |
| ----------------- | -------- |
| genome | |
| mito_name | |
| vcfanno_resources | |
| vcfanno_toml | |
| vep_cache_version | |
| vep_cache | |

#### Run the pipeline

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9 changes: 1 addition & 8 deletions main.nf
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Expand Up @@ -32,14 +32,7 @@ params.known_dbsnp_tbi = WorkflowMain.getGenomeAttribute(params,
params.known_indels = WorkflowMain.getGenomeAttribute(params, 'known_indels')
params.known_mills = WorkflowMain.getGenomeAttribute(params, 'known_mills')
params.ml_model = WorkflowMain.getGenomeAttribute(params, 'ml_model')
params.mt_backchain_shift = WorkflowMain.getGenomeAttribute(params, 'mt_backchain_shift')
params.mt_bwa_index_shift = WorkflowMain.getGenomeAttribute(params, 'mt_bwa_index_shift')
params.mt_bwamem2_index_shift = WorkflowMain.getGenomeAttribute(params, 'mt_bwamem2_index_shift')
params.mt_fasta_shift = WorkflowMain.getGenomeAttribute(params, 'mt_fasta_shift')
params.mt_fai_shift = WorkflowMain.getGenomeAttribute(params, 'mt_fai_shift')
params.mt_intervals = WorkflowMain.getGenomeAttribute(params, 'mt_intervals')
params.mt_intervals_shift = WorkflowMain.getGenomeAttribute(params, 'mt_intervals_shift')
params.mt_sequence_dictionary_shift = WorkflowMain.getGenomeAttribute(params, 'mt_sequence_dictionary_shift')
params.mt_fasta = WorkflowMain.getGenomeAttribute(params, 'mt_fasta')
params.reduced_penetrance = WorkflowMain.getGenomeAttribute(params, 'reduced_penetrance')
params.sequence_dictionary = WorkflowMain.getGenomeAttribute(params, 'sequence_dictionary')
params.score_config_snv = WorkflowMain.getGenomeAttribute(params, 'score_config_snv')
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7 changes: 6 additions & 1 deletion modules.json
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Expand Up @@ -145,6 +145,11 @@
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gatk4/shiftfasta": {
"branch": "master",
"git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
"installed_by": ["modules"]
},
"gatk4/splitintervals": {
"branch": "master",
"git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
Expand Down Expand Up @@ -262,7 +267,7 @@
},
"samtools/faidx": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
"installed_by": ["modules"]
},
"samtools/index": {
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66 changes: 66 additions & 0 deletions modules/nf-core/gatk4/shiftfasta/main.nf
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81 changes: 81 additions & 0 deletions modules/nf-core/gatk4/shiftfasta/meta.yml
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