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Dsl2 annotation #386

Merged
merged 23 commits into from
Jun 29, 2021
Merged

Dsl2 annotation #386

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a7b829f
feat: remove no longer used files
maxulysse Jun 8, 2021
2b705c9
feat: move modules from local to nf-core
maxulysse Jun 8, 2021
81bcdcb
Merge branch 'dsl2' into dsl2_annotation
maxulysse Jun 11, 2021
e8570cb
fix: restore samtools to 1.12
maxulysse Jun 11, 2021
531eecc
Merge branch 'dsl2_annotation' of github.com:maxulysse/nf-core_sarek …
maxulysse Jun 11, 2021
8205da4
Merge remote-tracking branch 'upstream/dsl2' into dsl2_annotation
maxulysse Jun 18, 2021
30bf2f4
feat: add annotation
maxulysse Jun 18, 2021
d79d39b
fix: update json
maxulysse Jun 18, 2021
cca46d7
feat: add tests for annotation
maxulysse Jun 18, 2021
df4fb5a
fix: output
maxulysse Jun 18, 2021
d6a6f03
fix: merge + add tests
maxulysse Jun 23, 2021
7f886cb
feat: containers à la carte
maxulysse Jun 23, 2021
01a0293
feat: move args to conf/modules.config
maxulysse Jun 23, 2021
8b9812e
fix: get rid of warning message
maxulysse Jun 23, 2021
a3ab368
fix: code polishing
maxulysse Jun 23, 2021
cc749c5
feat: add tests for subworkflow annotate
maxulysse Jun 24, 2021
44594c5
fix: annotate tests
maxulysse Jun 24, 2021
3da89f7
code polishing
maxulysse Jun 24, 2021
11f39a6
feat: add test for snpeff_annotate subworkflow
maxulysse Jun 24, 2021
b0982ac
feat: add test for vep_annotate subworkflow
maxulysse Jun 24, 2021
bf2a182
fix: update meta.yml file for snpEff
maxulysse Jun 25, 2021
1a9d53c
fix: update meta.yml file for VEP
maxulysse Jun 25, 2021
b7781ea
chores: update files
maxulysse Jun 25, 2021
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109 changes: 0 additions & 109 deletions .circleci/config.yml
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -26,7 +26,7 @@ jobs:
nxf_ver: ['21.04.0', '']
engine: ['docker']

test: ['default', 'aligner', 'gatk4_spark', 'targeted', 'tumor_normal_pair', 'variant_calling']
test: ['default', 'aligner', 'gatk4_spark', 'targeted', 'tumor_normal_pair', 'variant_calling', 'annotation']
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand Down
20 changes: 10 additions & 10 deletions conf/base.config
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Expand Up @@ -41,19 +41,19 @@ process {
time = { check_resource( 20.h * task.attempt) }
}

// withName:CONCAT_VCF {
// // For unknown reasons, CONCAT_VCF sometimes fails with SIGPIPE
// // (exit code 141). Rerunning the process will usually work.
// errorStrategy = {task.exitStatus == 141 ? 'retry' : 'terminate'}
// }
withLabel:FASTQC {
withName:CONCAT_VCF {
// For unknown reasons, CONCAT_VCF sometimes fails with SIGPIPE
// (exit code 141). Rerunning the process will usually work.
errorStrategy = {task.exitStatus == 141 ? 'retry' : 'terminate'}
}
withName:FASTQC {
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
}
withLabel:BWAMEM2_MEM {
withName:BWAMEM2_MEM {
memory = {check_resource(60.GB * task.attempt)}
time = {check_resource(48.h * task.attempt)}
}
// withName:MULTIQC {
// errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
// }
withName:MULTIQC {
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
}
}
31 changes: 18 additions & 13 deletions conf/genomes.config
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Expand Up @@ -27,8 +27,9 @@ params {
known_indels_index = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
mappability = "${params.genomes_base}/out100m2_hg19.gem"
snpeff_db = 'GRCh37.75'
species = 'homo_sapiens'
vep_cache_version = '99'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
}
'GRCh38' {
ac_loci = "${params.genomes_base}/1000G_phase3_GRCh38_maf0.3.loci"
Expand All @@ -47,9 +48,10 @@ params {
known_indels = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
known_indels_index = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
mappability = "${params.genomes_base}/out100m2_hg38.gem"
snpeff_db = 'GRCh38.86'
species = 'homo_sapiens'
vep_cache_version = '99'
snpeff_db = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
}
'minimalGRCh37' {
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
Expand All @@ -60,9 +62,10 @@ params {
germline_resource = "${params.genomes_base}/gnomAD.r2.1.1.GRCh37.small.PASS.AC.AF.only.vcf.gz"
intervals = "${params.genomes_base}/small.intervals"
known_indels = "${params.genomes_base}/Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz"
snpeff_db = 'GRCh37.87'
species = 'homo_sapiens'
vep_cache_version = '99'
snpeff_db = 'GRCh37.75'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
}
'smallerGRCh37' {
fasta = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
Expand All @@ -72,8 +75,9 @@ params {
dbsnp = "${params.genomes_base}/dbsnp_146_hg38_chr20_tso-only.vcf.gz"
fasta = "${params.genomes_base}/Homo_sapiens_assembly38_chr20.fasta"
known_indels = "${params.genomes_base}/Mills_and_1000G_gold_standard_indels_hg38_chr20.vcf.gz"
snpeff_db = 'GRCh38.86'
species = 'homo_sapiens'
snpeff_db = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '99'
}
'custom' {
Expand All @@ -85,9 +89,10 @@ params {
fasta_fai = "${params.genomes_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai"
germline_resource = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz"
known_indels = "${params.genomes_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
snpeff_db = 'GRCh38.86'
species = 'homo_sapiens'
vep_cache_version = '99'
snpeff_db = 'GRCh38.99'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '104'
}
}
}
26 changes: 15 additions & 11 deletions conf/igenomes.config
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Expand Up @@ -28,8 +28,9 @@ params {
known_indels_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
snpeff_db = 'GRCh37.75'
species = 'homo_sapiens'
vep_cache_version = '99'
vep_cache_version = '104'
vep_genome = 'GRCh37'
vep_species = 'homo_sapiens'
}
'Ensembl.GRCh37' {
fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
Expand All @@ -52,9 +53,10 @@ params {
known_indels = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
known_indels_index = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
mappability = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem"
snpeff_db = 'GRCh38.86'
species = 'homo_sapiens'
vep_cache_version = '99'
snpeff_db = 'GRCh38.99'
vep_cache_version = '104'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
}
'NCBI.GRCh38' {
fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
Expand All @@ -73,9 +75,10 @@ params {
known_indels = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
known_indels_index = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
mappability = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
snpeff_db = 'GRCm38.86'
species = 'mus_musculus'
vep_cache_version = '99'
snpeff_db = 'GRCm38.99'
vep_cache_version = '102'
vep_genome = 'GRCm38'
vep_species = 'mus_musculus'
}
'TAIR10' {
bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
Expand All @@ -96,9 +99,10 @@ params {
'WBcel235' {
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
snpeff_db = 'WBcel235.86'
species = 'caenorhabditis_elegans'
vep_cache_version = '99'
snpeff_db = 'WBcel235.99'
vep_cache_version = '104'
vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'
}
'ce10' {
bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa.{amb,ann,bwt,pac,sa}"
Expand Down
33 changes: 32 additions & 1 deletion conf/modules.config
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Expand Up @@ -27,7 +27,8 @@ params {
publish_dir = 'reference'
publish_files = false
}
'index_target_bed' {
'bgziptabix_target_bed' {
suffix = '.bed'
publish_dir = 'reference'
publish_files = false
}
Expand Down Expand Up @@ -200,6 +201,36 @@ params {
publish_dir = 'variant_calling'
publish_files = ['vcf.gz':'strelka', 'vcf.gz.tbi':'strelka']
}
// ANNOTATE
'snpeff' {
args = '-nodownload -canon -v'
publish_files = false
tag_base = '5.0'
}
'bgziptabix_snpeff' {
publish_dir = 'annotation'
suffix = '_snpEff.ann'
publish_by_meta = true
}
'merge_vep' {
args = '--everything --filter_common --per_gene --total_length --offline'
publish_files = false
}
'bgziptabix_merge_vep' {
publish_dir = 'annotation'
suffix = '_snpEff_VEP.ann'
publish_by_meta = true
}
'vep' {
args = '--everything --filter_common --per_gene --total_length --offline'
publish_files = false
tag_base = '104.3'
}
'bgziptabix_vep' {
publish_dir = 'annotation'
suffix = '_VEP.ann'
publish_by_meta = true
}
// QC_TRIM
'fastqc' {
args = '--quiet'
Expand Down
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