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Include new module ASCAT #606

Merged
merged 37 commits into from
Jul 1, 2022
Merged

Include new module ASCAT #606

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7a1b0ce
add ascat locally
SusiJo Jun 21, 2022
636f919
install unzip
SusiJo Jun 22, 2022
5bb319f
add ascat genome string
SusiJo Jun 22, 2022
5420559
add unzip
SusiJo Jun 22, 2022
0812d16
adjust format
SusiJo Jun 22, 2022
7e569cd
add ascat stuff
SusiJo Jun 22, 2022
77618e9
fix channels
SusiJo Jun 22, 2022
60205c3
quick fixes
SusiJo Jun 22, 2022
e311941
quick fixes
SusiJo Jun 22, 2022
3aa4c01
quick fixes
SusiJo Jun 22, 2022
052c40f
fix new params
SusiJo Jun 22, 2022
e2d97d5
fix ascat_params
SusiJo Jun 22, 2022
798a43e
quick fixes
SusiJo Jun 22, 2022
0165763
test empty channel
SusiJo Jun 23, 2022
fe40602
quick fixes
SusiJo Jun 23, 2022
110a954
adjust gender, add stuff to test ascat locally
SusiJo Jun 23, 2022
762b2cc
Merge remote-tracking branch 'upstream/dev' into ascat
SusiJo Jun 23, 2022
8c306eb
installed new module ascat
SusiJo Jun 24, 2022
438b94c
change order of channels
SusiJo Jun 24, 2022
89833a2
fix userEmulation closure
SusiJo Jun 24, 2022
574f7bd
push working version
SusiJo Jun 24, 2022
79b95c0
updated to use igenomes
SusiJo Jun 24, 2022
dd0426d
fix loci input + add warnings
SusiJo Jun 24, 2022
6b60a92
add warnings
SusiJo Jun 24, 2022
125e5a3
add download link for reference files
SusiJo Jun 24, 2022
3ff0eb0
Merge remote-tracking branch 'origin/dev' into ascat
SusiJo Jun 24, 2022
66cf52a
Merge branch 'ascat' of https://github.com/SusiJo/sarek into ascat
SusiJo Jun 24, 2022
eee5a24
add params, ci tests, rm deprec. scripts, ch doc
SusiJo Jun 27, 2022
2411d1b
Merge remote-tracking branch 'origin/dev' into ascat
SusiJo Jun 27, 2022
15d06a2
quick fixes
SusiJo Jun 27, 2022
7ad291b
fix input channels of pair_var_calling
SusiJo Jun 27, 2022
8250155
update ascat module + docs
SusiJo Jun 28, 2022
d6fa962
making things prettier
SusiJo Jun 28, 2022
139f98e
Merge remote-tracking branch 'origin/dev' into ascat
SusiJo Jun 29, 2022
c5d5097
incorporate PR feedback
SusiJo Jun 29, 2022
b1fb569
Merge remote-tracking branch 'origin/dev' into ascat
SusiJo Jul 1, 2022
f09de9a
fixed ci tests
SusiJo Jul 1, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -69,6 +69,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#581](https://github.com/nf-core/sarek/pull/581) - `TIDDIT` is updated to `3.1.0`
- [#593](https://github.com/nf-core/sarek/pull/593) - update `ensembl-vep` cache version and module
- [#600](https://github.com/nf-core/sarek/pull/600) - Remove `TODO` in awsfulltest
- [#606](https://github.com/nf-core/sarek/pull/606) - Updated `ASCAT` to version `3.0` as module

### Fixed

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14 changes: 10 additions & 4 deletions conf/igenomes.config
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Expand Up @@ -12,8 +12,11 @@ params {
// illumina iGenomes reference file paths
genomes {
'GATK.GRCh37' {
ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci"
ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/1000G_phase3_20130502_SNP_maf0.3.loci.gc"
ascat_alleles = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_alleles_hg19.zip"
ascat_genome = 'hg19'
ascat_loci = "${params.ascat_loci}" //test does not work with chr_annotated files"${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_loci_hg19.zip"
ascat_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/GC_G1000_hg19.zip"
ascat_loci_rt = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/RT_G1000_hg19.zip"
bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/"
chr_dir = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes"
dbsnp = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf"
Expand All @@ -34,8 +37,11 @@ params {
vep_species = 'homo_sapiens'
}
'GATK.GRCh38' {
ac_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci"
ac_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/1000G_phase3_GRCh38_maf0.3.loci.gc"
ascat_alleles = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_alleles_hg38.zip"
ascat_genome = 'hg38'
ascat_loci = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/G1000_loci_hg38.zip"
ascat_loci_gc = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/GC_G1000_hg38.zip"
ascat_loci_rt = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/ASCAT/RT_G1000_hg38.zip"
bwa = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/"
bwamem2 = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/"
dragmap = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/"
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40 changes: 21 additions & 19 deletions conf/modules.config
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Expand Up @@ -928,25 +928,27 @@ process{
// PAIR_VARIANT_CALLING

//ASCAT
if (params.tools && params.tools.contains('ascat')) {
withName: 'ASCAT' {
ext.args = {
[
"gender": meta.sex,
//"genomeVersion": "hg19"
//"purity": (optional),
//"ploidy": params.ploidy,
//"gc_files": (optional),
//"minCounts": (optional),
//"chrom_names": (optional),
//"min_base_qual": (optional),
//"min_map_qual": (optional),
//"ref_fasta": (optional),
//"skip_allele_counting_tumour": (optional),
//"skip_allele_counting_normal": (optional)
]
}
}
withName: 'ASCAT' {

ext.args = {[
"gender": meta.gender,
"genomeVersion": params.ascat_genome,
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"purity": params.ascat_purity,
"ploidy": params.ploidy,
//"minCounts": (optional),
"chrom_names": 'c("21","22")' //,
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//"min_base_qual": (optional),
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//"min_map_qual": (optional),
//"skip_allele_counting_tumour": (optional),
//"skip_allele_counting_normal": (optional)
]}
ext.when = { params.tools && params.tools.contains('ascat') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/${meta.id}/ascat" },
pattern: "*{png,txt}"
]

}

//CONTROLFREEC
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17 changes: 17 additions & 0 deletions conf/test.config
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Expand Up @@ -150,6 +150,23 @@ profiles {

params.nucleotides_per_second = 20
}
// can only be tested locally due to too large cram files for GHA
// download corresponding input files (ascat_somatic.csv) from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/
// test works only without chromosome annotated loci files available at https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
tools_somatic_ascat{
params.input = "${baseDir}/tests/csv/3.0/ascat_somatic.csv"
params.chr_dir = params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir']
params.ascat_loci = "/mnt/volume/repos/modules/test_ascat2/G1000_loci_hg19.zip"
params.germline_resource = params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz']
params.intervals = params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed']
params.step = 'variant_calling'
params.joint_germline = true
params.wes = false
params.tools = 'ascat'
params.igenomes_ignore = false
params.genome = 'GATK.GRCh37'

}
trimming {
params.clip_r1 = 1
params.clip_r2 = 1
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7 changes: 5 additions & 2 deletions main.nf
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Expand Up @@ -27,8 +27,11 @@ nextflow.enable.dsl = 2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

params.ac_loci = WorkflowMain.getGenomeAttribute(params, 'ac_loci')
params.ac_loci_gc = WorkflowMain.getGenomeAttribute(params, 'ac_loci_gc')
params.ascat_alleles = WorkflowMain.getGenomeAttribute(params, 'ascat_alleles')
params.ascat_genome = WorkflowMain.getGenomeAttribute(params, 'ascat_genome')
params.ascat_loci = WorkflowMain.getGenomeAttribute(params, 'ascat_loci')
params.ascat_loci_gc = WorkflowMain.getGenomeAttribute(params, 'ascat_loci_gc')
params.ascat_loci_rt = WorkflowMain.getGenomeAttribute(params, 'ascat_loci_rt')
params.bwa = WorkflowMain.getGenomeAttribute(params, 'bwa')
params.bwamem2 = WorkflowMain.getGenomeAttribute(params, 'bwamem2')
params.chr_dir = WorkflowMain.getGenomeAttribute(params, 'chr_dir')
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6 changes: 6 additions & 0 deletions modules.json
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Expand Up @@ -3,6 +3,9 @@
"homePage": "https://github.com/nf-core/sarek",
"repos": {
"nf-core/modules": {
"ascat": {
"git_sha": "7daba6a13f8052761b655cabcd0047e0e306ce12"
},
"bcftools/sort": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
Expand Down Expand Up @@ -231,6 +234,9 @@
"untar": {
"git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
},
"unzip": {
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
},
"vcftools": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}
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196 changes: 196 additions & 0 deletions modules/nf-core/modules/ascat/main.nf
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