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FriederikeHanssenFriederikeHanssen
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remove enum list, resolve merge conflicts
2 parents 10c9281 + 9683205 commit 7269a06

14 files changed

Lines changed: 229 additions & 143 deletions

‎.github/workflows/ci.yml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -51,6 +51,7 @@ jobs:
5151
- "save_bam_mapped"
5252
- "save_output_as_bam"
5353
- "skip_markduplicates"
54+
- "skip_qc"
5455
- "split_fastq"
5556
- "strelka"
5657
- "strelkabp"

‎CHANGELOG.md‎

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Original file line numberDiff line numberDiff line change
@@ -88,6 +88,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
8888
- [#632](https://github.com/nf-core/sarek/pull/632) - Update `VEP` version to `106.1` and cache up to `106`
8989
- [#618](https://github.com/nf-core/sarek/pull/618) - Update `multiqc` module update test yml files
9090
- [#618](https://github.com/nf-core/sarek/pull/618) - Update test yml files
91+
- [#644](https://github.com/nf-core/sarek/pull/644) - Use `-Y` for `bwa-mem(2)` and remove `-M`
92+
- [#645](https://github.com/nf-core/sarek/pull/645) - Merge `tests/nextflow.config` in `conf/test.config`
9193
- [#646](https://github.com/nf-core/sarek/pull/646) - Update `nextflow_schema.json` to reflect new parameters and functions, removes `--annotation_cache`, removes `--ascat_chromosomes`
9294

9395
### Fixed
@@ -134,6 +136,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
134136
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix issue with tiddit [#621](https://github.com/nf-core/sarek/issues/621)
135137
- [#618](https://github.com/nf-core/sarek/pull/618) - Fix channel issue with `targets.bed` in prepare_intervals
136138
- [#634](https://github.com/nf-core/sarek/pull/634) - Fix issue with samtools/mosdepth plots in multiqc_report
139+
- [#641](https://github.com/nf-core/sarek/pull/641) - Fix issue with duplicate substring in tools and skip_tools
137140

138141
### Deprecated
139142

‎conf/modules.config‎

Lines changed: 48 additions & 48 deletions
Large diffs are not rendered by default.

‎conf/test.config‎

Lines changed: 34 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -195,3 +195,37 @@ profiles {
195195
params.input = "${projectDir}/tests/csv/3.0/bam_for_remapping.csv"
196196
}
197197
}
198+
199+
process {
200+
withName:'FREEC_SOMATIC'{
201+
ext.args = {
202+
[
203+
"sample":[
204+
inputformat: 'pileup',
205+
mateorientation: 'FR'
206+
],
207+
"general" :[
208+
bedgraphoutput: "TRUE",
209+
noisydata: "TRUE",
210+
minexpectedgc: "0",
211+
readcountthreshold: "1",
212+
sex: meta.sex,
213+
window: "10",
214+
],
215+
"control":[
216+
inputformat: "pileup",
217+
mateorientation: "FR"
218+
]
219+
]
220+
}
221+
}
222+
223+
withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{
224+
//sample name from when the test data was generated
225+
ext.args = { "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample normal " }
226+
}
227+
228+
withName: 'FILTERVARIANTTRANCHES'{
229+
ext.args = { "--info-key CNN_1D --indel-tranche 0" }
230+
}
231+
}

‎subworkflows/local/annotate.nf‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -18,23 +18,23 @@ workflow ANNOTATE {
1818
vep_cache_version
1919
vep_cache
2020
vep_extra_files
21-
21+
2222
main:
2323
ch_reports = Channel.empty()
2424
ch_vcf_ann = Channel.empty()
2525
ch_tab_ann = Channel.empty()
2626
ch_json_ann = Channel.empty()
2727
ch_versions = Channel.empty()
2828

29-
if (tools.contains('merge') || tools.contains('snpeff')) {
29+
if (tools.split(',').contains('merge') || tools.split(',').contains('snpeff')) {
3030
ANNOTATION_SNPEFF(vcf, snpeff_db, snpeff_cache)
3131

3232
ch_reports = ch_reports.mix(ANNOTATION_SNPEFF.out.reports)
3333
ch_vcf_ann = ch_vcf_ann.mix(ANNOTATION_SNPEFF.out.vcf_tbi)
3434
ch_versions = ch_versions.mix(ANNOTATION_SNPEFF.out.versions.first())
3535
}
3636

37-
if (tools.contains('merge')) {
37+
if (tools.split(',').contains('merge')) {
3838
vcf_ann_for_merge = ANNOTATION_SNPEFF.out.vcf_tbi.map{ meta, vcf, tbi -> [meta, vcf] }
3939
ANNOTATION_MERGE(vcf_ann_for_merge, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files)
4040

@@ -43,7 +43,7 @@ workflow ANNOTATE {
4343
ch_versions = ch_versions.mix(ANNOTATION_MERGE.out.versions.first())
4444
}
4545

46-
if (tools.contains('vep')) {
46+
if (tools.split(',').contains('vep')) {
4747
ANNOTATION_ENSEMBLVEP(vcf, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files)
4848

4949
ch_reports = ch_reports.mix(ANNOTATION_ENSEMBLVEP.out.reports)

‎subworkflows/local/germline_variant_calling.nf‎

Lines changed: 9 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -42,6 +42,7 @@ workflow GERMLINE_VARIANT_CALLING {
4242
strelka_vcf = Channel.empty()
4343
tiddit_vcf = Channel.empty()
4444

45+
println tools
4546
// Remap channel with intervals
4647
cram_recalibrated_intervals = cram_recalibrated.combine(intervals)
4748
.map{ meta, cram, crai, intervals, num_intervals ->
@@ -65,7 +66,7 @@ workflow GERMLINE_VARIANT_CALLING {
6566
cram, crai, bed_new, tbi_new]
6667
}
6768

68-
if(params.tools.contains('mpileup')){
69+
if(tools.split(',').contains('mpileup')){
6970
cram_intervals_no_index = cram_recalibrated_intervals
7071
.map { meta, cram, crai, intervals ->
7172
[meta, cram, intervals]
@@ -79,7 +80,7 @@ workflow GERMLINE_VARIANT_CALLING {
7980

8081
// CNVKIT
8182

82-
if(tools.contains('cnvkit')){
83+
if(tools.split(',').contains('cnvkit')){
8384
cram_recalibrated_cnvkit_germline = cram_recalibrated
8485
.map{ meta, cram, crai ->
8586
[meta, [], cram]
@@ -94,15 +95,15 @@ workflow GERMLINE_VARIANT_CALLING {
9495
}
9596

9697
// DEEPVARIANT
97-
if(tools.contains('deepvariant')){
98+
if(tools.split(',').contains('deepvariant')){
9899
RUN_DEEPVARIANT(cram_recalibrated_intervals, dict, fasta, fasta_fai)
99100

100101
deepvariant_vcf = Channel.empty().mix(RUN_DEEPVARIANT.out.deepvariant_vcf,RUN_DEEPVARIANT.out.deepvariant_gvcf)
101102
ch_versions = ch_versions.mix(RUN_DEEPVARIANT.out.versions)
102103
}
103104

104105
// FREEBAYES
105-
if (tools.contains('freebayes')){
106+
if (tools.split(',').contains('freebayes')){
106107
// Remap channel for Freebayes
107108
cram_recalibrated_intervals_freebayes = cram_recalibrated_intervals
108109
.map{ meta, cram, crai, intervals ->
@@ -115,7 +116,7 @@ workflow GERMLINE_VARIANT_CALLING {
115116
}
116117

117118
// HAPLOTYPECALLER
118-
if (tools.contains('haplotypecaller')){
119+
if (tools.split(',').contains('haplotypecaller')){
119120
RUN_HAPLOTYPECALLER(cram_recalibrated_intervals,
120121
fasta,
121122
fasta_fai,
@@ -131,7 +132,7 @@ workflow GERMLINE_VARIANT_CALLING {
131132
}
132133

133134
// MANTA
134-
if (tools.contains('manta')){
135+
if (tools.split(',').contains('manta')){
135136
RUN_MANTA_GERMLINE (cram_recalibrated_intervals_gz_tbi,
136137
dict,
137138
fasta,
@@ -142,7 +143,7 @@ workflow GERMLINE_VARIANT_CALLING {
142143
}
143144

144145
// STRELKA
145-
if (tools.contains('strelka')){
146+
if (tools.split(',').contains('strelka')){
146147
RUN_STRELKA_SINGLE(cram_recalibrated_intervals_gz_tbi,
147148
dict,
148149
fasta,
@@ -153,7 +154,7 @@ workflow GERMLINE_VARIANT_CALLING {
153154
}
154155

155156
//TIDDIT
156-
if (tools.contains('tiddit')){
157+
if (tools.split(',').contains('tiddit')){
157158
RUN_TIDDIT(cram_recalibrated,
158159
fasta,
159160
bwa)

‎subworkflows/local/pair_variant_calling.nf‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,7 @@ workflow PAIR_VARIANT_CALLING {
7575

7676
}
7777

78-
if (tools.contains('ascat')){
78+
if (tools.split(',').contains('ascat')){
7979

8080
RUN_ASCAT_SOMATIC( cram_pair,
8181
allele_files,
@@ -89,7 +89,7 @@ workflow PAIR_VARIANT_CALLING {
8989

9090
}
9191

92-
if (tools.contains('controlfreec')){
92+
if (tools.split(',').contains('controlfreec')){
9393
cram_normal_intervals_no_index = cram_pair_intervals
9494
.map {meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals ->
9595
[meta, normal_cram, intervals]
@@ -124,7 +124,7 @@ workflow PAIR_VARIANT_CALLING {
124124
ch_versions = ch_versions.mix(RUN_CONTROLFREEC_SOMATIC.out.versions)
125125
}
126126

127-
if (tools.contains('cnvkit')){
127+
if (tools.split(',').contains('cnvkit')){
128128
cram_pair_cnvkit_somatic = cram_pair
129129
.map{meta, normal_cram, normal_crai, tumor_cram, tumor_crai ->
130130
[meta, tumor_cram, normal_cram]
@@ -137,14 +137,14 @@ workflow PAIR_VARIANT_CALLING {
137137
[])
138138
}
139139

140-
if (tools.contains('freebayes')){
140+
if (tools.split(',').contains('freebayes')){
141141
RUN_FREEBAYES_SOMATIC(cram_pair_intervals, dict, fasta, fasta_fai)
142142

143143
freebayes_vcf = RUN_FREEBAYES_SOMATIC.out.freebayes_vcf
144144
ch_versions = ch_versions.mix(RUN_FREEBAYES_SOMATIC.out.versions)
145145
}
146146

147-
if (tools.contains('manta')) {
147+
if (tools.split(',').contains('manta')) {
148148
RUN_MANTA_SOMATIC( cram_pair_intervals_gz_tbi,
149149
dict,
150150
fasta,
@@ -156,9 +156,9 @@ workflow PAIR_VARIANT_CALLING {
156156
ch_versions = ch_versions.mix(RUN_MANTA_SOMATIC.out.versions)
157157
}
158158

159-
if (tools.contains('strelka')) {
159+
if (tools.split(',').contains('strelka')) {
160160

161-
if (tools.contains('manta')) {
161+
if (tools.split(',').contains('manta')) {
162162
cram_pair_strelka = cram_pair.join(manta_candidate_small_indels_vcf)
163163
.join(manta_candidate_small_indels_vcf_tbi)
164164
.combine(intervals_bed_gz_tbi)
@@ -188,15 +188,15 @@ workflow PAIR_VARIANT_CALLING {
188188
ch_versions = ch_versions.mix(RUN_STRELKA_SOMATIC.out.versions)
189189
}
190190

191-
if (tools.contains('msisensorpro')) {
191+
if (tools.split(',').contains('msisensorpro')) {
192192

193193
cram_pair_msisensor = cram_pair.combine(intervals_bed_combined)
194194
MSISENSORPRO_MSI_SOMATIC(cram_pair_msisensor, fasta, msisensorpro_scan)
195195
ch_versions = ch_versions.mix(MSISENSORPRO_MSI_SOMATIC.out.versions)
196196
msisensorpro_output = msisensorpro_output.mix(MSISENSORPRO_MSI_SOMATIC.out.output_report)
197197
}
198198

199-
if (tools.contains('mutect2')) {
199+
if (tools.split(',').contains('mutect2')) {
200200
cram_pair_mutect2 = cram_pair_intervals.map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals ->
201201
[meta, [normal_cram, tumor_cram], [normal_crai, tumor_crai], intervals]
202202
}
@@ -216,7 +216,7 @@ workflow PAIR_VARIANT_CALLING {
216216
}
217217

218218
//TIDDIT
219-
if (tools.contains('tiddit')){
219+
if (tools.split(',').contains('tiddit')){
220220
cram_normal = cram_pair.map{meta, normal_cram, normal_crai, tumor_cram, tumor_crai ->
221221
[meta, normal_cram, normal_crai]
222222
}

‎subworkflows/local/tumor_variant_calling.nf‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -66,7 +66,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
6666
cram, crai, bed_new, tbi_new]
6767
}
6868

69-
if (tools.contains('mpileup') || tools.contains('controlfreec')){
69+
if (tools.split(',').contains('mpileup') || tools.split(',').contains('controlfreec')){
7070
cram_intervals_no_index = cram_recalibrated_intervals.map { meta, cram, crai, intervals ->
7171
[meta, cram, intervals]
7272
}
@@ -75,7 +75,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
7575
ch_versions = ch_versions.mix(RUN_MPILEUP.out.versions)
7676
}
7777

78-
if (tools.contains('controlfreec')){
78+
if (tools.split(',').contains('controlfreec')){
7979
controlfreec_input = RUN_MPILEUP.out.mpileup
8080
.map{ meta, pileup_tumor ->
8181
[meta, [], pileup_tumor, [], [], [], []]
@@ -93,7 +93,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
9393
ch_versions = ch_versions.mix(RUN_CONTROLFREEC_TUMORONLY.out.versions)
9494
}
9595

96-
if(tools.contains('cnvkit')){
96+
if(tools.split(',').contains('cnvkit')){
9797
cram_recalibrated_cnvkit_tumoronly = cram_recalibrated
9898
.map{ meta, cram, crai ->
9999
[meta, cram, []]
@@ -108,7 +108,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
108108
ch_versions = ch_versions.mix(RUN_CNVKIT_TUMORONLY.out.versions)
109109
}
110110

111-
if (tools.contains('freebayes')){
111+
if (tools.split(',').contains('freebayes')){
112112
// Remap channel for Freebayes
113113
cram_recalibrated_intervals_freebayes = cram_recalibrated_intervals
114114
.map{ meta, cram, crai, intervals ->
@@ -121,7 +121,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
121121
ch_versions = ch_versions.mix(RUN_FREEBAYES.out.versions)
122122
}
123123

124-
if (tools.contains('mutect2')) {
124+
if (tools.split(',').contains('mutect2')) {
125125
GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING(cram_recalibrated_intervals,
126126
fasta,
127127
fasta_fai,
@@ -135,7 +135,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
135135
ch_versions = ch_versions.mix(GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING.out.versions)
136136
}
137137

138-
if (tools.contains('manta')){
138+
if (tools.split(',').contains('manta')){
139139
RUN_MANTA_TUMORONLY(cram_recalibrated_intervals_gz_tbi,
140140
dict,
141141
fasta,
@@ -145,7 +145,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
145145
ch_versions = ch_versions.mix(RUN_MANTA_TUMORONLY.out.versions)
146146
}
147147

148-
if (tools.contains('strelka')) {
148+
if (tools.split(',').contains('strelka')) {
149149
RUN_STRELKA_SINGLE(cram_recalibrated_intervals_gz_tbi,
150150
dict,
151151
fasta,
@@ -156,7 +156,7 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
156156
}
157157

158158
//TIDDIT
159-
if (tools.contains('tiddit')){
159+
if (tools.split(',').contains('tiddit')){
160160
RUN_TIDDIT(cram_recalibrated,
161161
fasta,
162162
bwa)

‎tests/nextflow.config‎

Lines changed: 0 additions & 34 deletions
This file was deleted.

‎tests/test_bam_remap.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
- name: Run alignment to fastq and then remap on bam files
2-
command: nextflow run main.nf -profile test,alignment_to_fastq,docker -c ./tests/nextflow.config
2+
command: nextflow run main.nf -profile test,alignment_to_fastq,docker
33
tags:
44
- alignment_to_fastq
55

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