Skip to content

Commit 1c43f34

Browse files
maxulyssemaxulysse
committed
code polish
1 parent 68687ef commit 1c43f34

5 files changed

Lines changed: 42 additions & 40 deletions

File tree

‎subworkflows/local/annotate.nf‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -8,15 +8,15 @@ include { ANNOTATION_ENSEMBLVEP } from '../nf-core/annotatio
88

99
workflow ANNOTATE {
1010
take:
11-
vcf // channel: [ val(meta), vcf ]
12-
tools
13-
snpeff_db
14-
snpeff_cache
15-
vep_genome
16-
vep_species
17-
vep_cache_version
18-
vep_cache
19-
vep_extra_files
11+
vcf // channel: [ val(meta), vcf ]
12+
tools // Mandatory, list of tools to apply
13+
snpeff_db
14+
snpeff_cache
15+
vep_genome
16+
vep_species
17+
vep_cache_version
18+
vep_cache
19+
vep_extra_files
2020

2121
main:
2222
ch_reports = Channel.empty()

‎subworkflows/local/germline_variant_calling.nf‎

Lines changed: 18 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -7,21 +7,22 @@ include { RUN_FREEBAYES } from '../nf-core/variantcalling/freebayes/main.n
77
include { RUN_HAPLOTYPECALLER } from '../nf-core/variantcalling/haplotypecaller/main.nf'
88
include { RUN_MANTA_GERMLINE } from '../nf-core/variantcalling/manta/germline/main.nf'
99
include { RUN_STRELKA_SINGLE } from '../nf-core/variantcalling/strelka/single/main.nf'
10-
include { RUN_CNVKIT_GERMLINE } from '../nf-core/variantcalling/cnvkit/germline/main.nf'
10+
include { RUN_CNVKIT_GERMLINE } from '../nf-core/variantcalling/cnvkit/germline/main.nf'
1111
//include { TIDDIT } from './variantcalling/tiddit.nf'
1212

1313
workflow GERMLINE_VARIANT_CALLING {
1414
take:
15-
cram_recalibrated // channel: [mandatory] cram
16-
dbsnp // channel: [mandatory] dbsnp
17-
dbsnp_tbi // channel: [mandatory] dbsnp_tbi
18-
dict // channel: [mandatory] dict
19-
fasta // channel: [mandatory] fasta
20-
fasta_fai // channel: [mandatory] fasta_fai
21-
intervals // channel: [mandatory] intervals/target regions
22-
intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed
23-
intervals_bed_combined // channel: [mandatory] intervals/target regions in one file unzipped
24-
// joint_germline // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment
15+
tools // Mandatory, list of tools to apply
16+
cram_recalibrated // channel: [mandatory] cram
17+
dbsnp // channel: [mandatory] dbsnp
18+
dbsnp_tbi // channel: [mandatory] dbsnp_tbi
19+
dict // channel: [mandatory] dict
20+
fasta // channel: [mandatory] fasta
21+
fasta_fai // channel: [mandatory] fasta_fai
22+
intervals // channel: [mandatory] intervals/target regions
23+
intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed
24+
intervals_bed_combined // channel: [mandatory] intervals/target regions in one file unzipped
25+
// joint_germline // val: true/false on whether to run joint_germline calling, only works in combination with haplotypecaller at the moment
2526

2627
main:
2728

@@ -60,7 +61,7 @@ workflow GERMLINE_VARIANT_CALLING {
6061

6162
// CNVKIT
6263

63-
if(params.tools.contains('cnvkit')){
64+
if(tools.contains('cnvkit')){
6465
cram_recalibrated_cnvkit_germline = cram_recalibrated
6566
.map{ meta, cram, crai ->
6667
[meta, [], cram]
@@ -75,15 +76,15 @@ workflow GERMLINE_VARIANT_CALLING {
7576
}
7677

7778
// DEEPVARIANT
78-
if(params.tools.contains('deepvariant')){
79+
if(tools.contains('deepvariant')){
7980
RUN_DEEPVARIANT(cram_recalibrated_intervals, dict, fasta, fasta_fai)
8081

8182
deepvariant_vcf = Channel.empty().mix(RUN_DEEPVARIANT.out.deepvariant_vcf,RUN_DEEPVARIANT.out.deepvariant_gvcf)
8283
ch_versions = ch_versions.mix(RUN_DEEPVARIANT.out.versions)
8384
}
8485

8586
// FREEBAYES
86-
if (params.tools.contains('freebayes')){
87+
if (tools.contains('freebayes')){
8788
// Remap channel for Freebayes
8889
cram_recalibrated_intervals_freebayes = cram_recalibrated_intervals
8990
.map{ meta, cram, crai, intervals ->
@@ -96,7 +97,7 @@ workflow GERMLINE_VARIANT_CALLING {
9697
}
9798

9899
// HAPLOTYPECALLER
99-
if (params.tools.contains('haplotypecaller')){
100+
if (tools.contains('haplotypecaller')){
100101
RUN_HAPLOTYPECALLER(cram_recalibrated_intervals,
101102
fasta,
102103
fasta_fai,
@@ -110,7 +111,7 @@ workflow GERMLINE_VARIANT_CALLING {
110111
}
111112

112113
// MANTA
113-
if (params.tools.contains('manta')){
114+
if (tools.contains('manta')){
114115
RUN_MANTA_GERMLINE (cram_recalibrated_intervals_gz_tbi,
115116
dict,
116117
fasta,
@@ -121,7 +122,7 @@ workflow GERMLINE_VARIANT_CALLING {
121122
}
122123

123124
// STRELKA
124-
if (params.tools.contains('strelka')){
125+
if (tools.contains('strelka')){
125126
RUN_STRELKA_SINGLE(cram_recalibrated_intervals_gz_tbi,
126127
dict,
127128
fasta,

‎subworkflows/local/pair_variant_calling.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@ include { RUN_CNVKIT_SOMATIC } from '../nf-core/variantca
1111

1212
workflow PAIR_VARIANT_CALLING {
1313
take:
14-
tools
14+
tools // Mandatory, list of tools to apply
1515
cram_pair // channel: [mandatory] cram
1616
dbsnp // channel: [mandatory] dbsnp
1717
dbsnp_tbi // channel: [mandatory] dbsnp_tbi

‎subworkflows/local/tumor_variant_calling.nf‎

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -12,20 +12,20 @@ include { RUN_CNVKIT_TUMORONLY } from '../nf-core/variantcall
1212

1313
workflow TUMOR_ONLY_VARIANT_CALLING {
1414
take:
15-
tools // Mandatory, list of tools to apply
16-
cram_recalibrated // channel: [mandatory] cram
17-
dbsnp // channel: [mandatory] dbsnp
18-
dbsnp_tbi // channel: [mandatory] dbsnp_tbi
19-
dict // channel: [mandatory] dict
20-
fasta // channel: [mandatory] fasta
21-
fasta_fai // channel: [mandatory] fasta_fai
22-
intervals // channel: [mandatory] intervals/target regions
23-
intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed
15+
tools // Mandatory, list of tools to apply
16+
cram_recalibrated // channel: [mandatory] cram
17+
dbsnp // channel: [mandatory] dbsnp
18+
dbsnp_tbi // channel: [mandatory] dbsnp_tbi
19+
dict // channel: [mandatory] dict
20+
fasta // channel: [mandatory] fasta
21+
fasta_fai // channel: [mandatory] fasta_fai
22+
intervals // channel: [mandatory] intervals/target regions
23+
intervals_bed_gz_tbi // channel: [mandatory] intervals/target regions index zipped and indexed
2424
intervals_bed_combined // channel: [mandatory] intervals/target regions in one file unzipped
25-
germline_resource // channel: [optional] germline_resource
26-
germline_resource_tbi // channel: [optional] germline_resource_tbi
27-
panel_of_normals // channel: [optional] panel_of_normals
28-
panel_of_normals_tbi // channel: [optional] panel_of_normals_tbi
25+
germline_resource // channel: [optional] germline_resource
26+
germline_resource_tbi // channel: [optional] germline_resource_tbi
27+
panel_of_normals // channel: [optional] panel_of_normals
28+
panel_of_normals_tbi // channel: [optional] panel_of_normals_tbi
2929
chr_files
3030
mappability
3131

‎workflows/sarek.nf‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -770,6 +770,7 @@ workflow SAREK {
770770

771771
// GERMLINE VARIANT CALLING
772772
GERMLINE_VARIANT_CALLING(
773+
params.tools,
773774
cram_variant_calling_status_normal,
774775
dbsnp,
775776
dbsnp_tbi,

0 commit comments

Comments
 (0)
⚡