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Update all modules (#39)
* Update all modules * Update snaps * Update Changelog * Language Server Stuff * Resolve comments
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Lines changed: 953 additions & 1004 deletions

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‎CHANGELOG.md‎

Lines changed: 8 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -15,12 +15,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
1515
- [#35](https://github.com/qbic-pipelines/vcftomaf/pull/35) - Template update to 3.2.0 (@famosab)
1616
- [#37](https://github.com/qbic-pipelines/vcftomaf/pull/37) - Template update to 3.2.1 (@famosab)
1717
- [#38](https://github.com/qbic-pipelines/vcftomaf/pull/38) - Template update to 3.5.1 (@famosab)
18+
- [#39](https://github.com/qbic-pipelines/vcftomaf/pull/39) - Update all modules (@famosab)
1819

1920
### `Dependencies`
2021

21-
| Dependency | Old version | New version |
22-
| ---------- | ----------- | ----------- |
23-
| MultiQC | 1.25.1 | 1.32 |
22+
| Dependency. | Old version | New version |
23+
| -------------- | ----------- | ----------- |
24+
| BCFtools | 1.20 | 1.22 |
25+
| Gunzip | 1.1 | 1.13 |
26+
| MultiQC | 1.25.1 | 1.33 |
27+
| Picard | 3.3.0 | 3.4.0 |
28+
| Tabix (HTSlib) | 1.20 | 1.21 |
2429

2530
### `Deprecated`
2631

‎conf/base.config‎

Lines changed: 22 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -10,9 +10,9 @@
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process {
1212

13-
cpus = { 1 * task.attempt }
14-
memory = { 6.GB * task.attempt }
15-
time = { 4.h * task.attempt }
13+
cpus = { 1 * task.attempt }
14+
memory = { 6.GB * task.attempt }
15+
time = { 4.h * task.attempt }
1616

1717
errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
1818
maxRetries = 1
@@ -23,43 +23,43 @@ process {
2323
// These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
2424
// If possible, it would be nice to keep the same label naming convention when
2525
// adding in your local modules too.
26-
withLabel:error_ignore {
26+
withLabel: error_ignore {
2727
errorStrategy = 'ignore'
2828
}
29-
withLabel:error_retry {
29+
withLabel: error_retry {
3030
errorStrategy = 'retry'
3131
maxRetries = 2
3232
}
33-
withLabel:process_single {
34-
cpus = { 1 }
33+
withLabel: process_single {
34+
cpus = { 1 }
3535
memory = { 6.GB * task.attempt }
36-
time = { 4.h * task.attempt }
36+
time = { 4.h * task.attempt }
3737
}
38-
withLabel:process_low {
39-
cpus = { 2 * task.attempt }
38+
withLabel: process_low {
39+
cpus = { 2 * task.attempt }
4040
memory = { 12.GB * task.attempt }
41-
time = { 4.h * task.attempt }
41+
time = { 4.h * task.attempt }
4242
}
43-
withLabel:process_medium {
44-
cpus = { 6 * task.attempt }
43+
withLabel: process_medium {
44+
cpus = { 6 * task.attempt }
4545
memory = { 36.GB * task.attempt }
46-
time = { 8.h * task.attempt }
46+
time = { 8.h * task.attempt }
4747
}
48-
withLabel:process_high {
49-
cpus = { 12 * task.attempt }
48+
withLabel: process_high {
49+
cpus = { 12 * task.attempt }
5050
memory = { 72.GB * task.attempt }
51-
time = { 16.h * task.attempt }
51+
time = { 16.h * task.attempt }
5252
}
53-
withLabel:process_long {
54-
time = { 20.h * task.attempt }
53+
withLabel: process_long {
54+
time = { 20.h * task.attempt }
5555
}
56-
withLabel:process_high_memory {
56+
withLabel: process_high_memory {
5757
memory = { 200.GB * task.attempt }
5858
}
59-
withLabel:error_ignore {
59+
withLabel: error_ignore {
6060
errorStrategy = 'ignore'
6161
}
62-
withLabel:error_retry {
62+
withLabel: error_retry {
6363
errorStrategy = 'retry'
6464
maxRetries = 2
6565
}

‎conf/igenomes.config‎

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Large diffs are not rendered by default.

‎conf/modules.config‎

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Original file line numberDiff line numberDiff line change
@@ -15,19 +15,21 @@ process {
1515
publishDir = [
1616
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
1717
mode: params.publish_dir_mode,
18-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
18+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
1919
]
2020

2121
withName: BCFTOOLS_VIEW {
22-
ext.args = { [ "",
23-
params.filter ? "-f PASS": "",
24-
"--output-type z"
25-
].join(" ").trim() }
22+
ext.args = {
23+
[
24+
"",
25+
params.filter ? "-f PASS" : "",
26+
"--output-type z",
27+
].join(" ").trim()
28+
}
2629
}
2730

2831
withName: GUNZIP {
29-
publishDir = [
30-
//specify to avoid publishing, overwritten otherwise
32+
publishDir = [
3133
enabled: false
3234
]
3335
}
@@ -37,61 +39,61 @@ process {
3739
[
3840
path: { "${params.outdir}/liftover/lifted/" },
3941
mode: params.publish_dir_mode,
40-
pattern: "*.lifted.vcf.gz"
42+
pattern: "*.lifted.vcf.gz",
4143
],
4244
[
4345
path: { "${params.outdir}/liftover/unlifted/" },
4446
mode: params.publish_dir_mode,
45-
pattern: "*.unlifted.vcf.gz"
47+
pattern: "*.unlifted.vcf.gz",
4648
],
4749
[
4850
path: { "${params.outdir}/liftover/logs/" },
4951
mode: params.publish_dir_mode,
50-
pattern: "*.log"
51-
]
52+
pattern: "*.log",
53+
],
5254
]
5355
}
5456

5557
withName: TABIX_TABIX {
56-
publishDir = [
57-
//specify to avoid publishing, overwritten otherwise
58+
publishDir = [
5859
enabled: false
5960
]
6061
}
6162

6263
withName: UNTAR {
63-
publishDir = [
64-
//specify to avoid publishing, overwritten otherwise
64+
publishDir = [
6565
enabled: false
6666
]
6767
}
6868

6969
withName: VCF2MAF {
70-
ext.args = { [ "",
71-
params.run_vep ? "" : "--inhibit-vep",
72-
meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
73-
meta.tumor_id ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}" : "",
74-
"--retain-fmt AD,AF,DP,GQ,GT,STR",
75-
"--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
76-
"--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
77-
"--any-allele",
78-
"--ncbi-build ${params.genome.tokenize('.')[-1]}",
79-
"--species homo_sapiens"
80-
].join(" ").trim() }
70+
ext.args = {
71+
[
72+
"",
73+
params.run_vep ? "" : "--inhibit-vep",
74+
meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
75+
meta.tumor_id ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}" : "",
76+
"--retain-fmt AD,AF,DP,GQ,GT,STR",
77+
"--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
78+
"--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
79+
"--any-allele",
80+
"--ncbi-build ${params.genome.tokenize('.')[-1]}",
81+
"--species homo_sapiens",
82+
].join(" ").trim()
83+
}
8184
publishDir = [
8285
path: { "${params.outdir}/maf" },
8386
mode: params.publish_dir_mode,
84-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
87+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
8588
]
8689
}
8790

88-
withName: 'MULTIQC' {
89-
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
91+
withName: MULTIQC {
92+
ext.args = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
9093
publishDir = [
9194
path: { "${params.outdir}/multiqc" },
9295
mode: params.publish_dir_mode,
93-
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
96+
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
9497
]
9598
}
96-
9799
}

‎conf/test.config‎

Lines changed: 6 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ process {
1414
resourceLimits = [
1515
cpus: 4,
1616
memory: '15.GB',
17-
time: '1.h'
17+
time: '1.h',
1818
]
1919
}
2020

@@ -23,10 +23,9 @@ params {
2323
config_profile_description = 'Minimal test dataset to check pipeline function'
2424

2525
// Input data
26-
input = "${projectDir}/tests/samplesheets/samplesheet.csv"
27-
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
28-
intervals = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
29-
genome = 'GATK.GRCh38'
30-
filter = false
31-
26+
input = "${projectDir}/tests/samplesheets/samplesheet.csv"
27+
fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
28+
intervals = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
29+
genome = 'GATK.GRCh38'
30+
filter = false
3231
}

‎main.nf‎

Lines changed: 48 additions & 63 deletions
Original file line numberDiff line numberDiff line change
@@ -17,6 +17,46 @@ include { VCFTOMAF } from './workflows/vcftomaf'
1717
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
1818
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
1919
include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
20+
/*
21+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
22+
RUN MAIN WORKFLOW
23+
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
24+
*/
25+
26+
workflow {
27+
//
28+
// SUBWORKFLOW: Run initialisation tasks
29+
//
30+
PIPELINE_INITIALISATION(
31+
params.version,
32+
params.validate_params,
33+
params.monochrome_logs,
34+
args,
35+
params.outdir,
36+
params.input,
37+
params.help,
38+
params.help_full,
39+
params.show_hidden,
40+
)
41+
42+
//
43+
// WORKFLOW: Run main workflow
44+
//
45+
QBICPIPELINES_VCFTOMAF(
46+
PIPELINE_INITIALISATION.out.samplesheet
47+
)
48+
49+
//
50+
PIPELINE_COMPLETION(
51+
params.email,
52+
params.email_on_fail,
53+
params.plaintext_email,
54+
params.outdir,
55+
params.monochrome_logs,
56+
params.hook_url,
57+
QBICPIPELINES_VCFTOMAF.out.multiqc_report,
58+
)
59+
}
2060

2161
/*
2262
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -28,97 +68,42 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_vcft
2868
// WORKFLOW: Run main analysis pipeline depending on type of input
2969
//
3070
workflow QBICPIPELINES_VCFTOMAF {
31-
3271
take:
3372
samplesheet // channel: samplesheet read in from --input
3473

3574
main:
36-
3775
//
3876
// SET PARAMETERS
3977
//
4078
params.fasta = getGenomeAttribute('fasta')
4179
params.dict = getGenomeAttribute('dict')
4280

4381
// Extra files
44-
intervals = params.intervals ? Channel.fromPath(params.intervals).collect() : Channel.value([])
45-
liftover_chain = params.liftover_chain ? Channel.fromPath(params.liftover_chain).collect() : Channel.value([])
82+
intervals = params.intervals ? channel.fromPath(params.intervals).collect() : channel.value([])
83+
liftover_chain = params.liftover_chain ? channel.fromPath(params.liftover_chain).collect() : channel.value([])
4684

4785
// FASTA
48-
fasta = params.fasta ? Channel.fromPath(params.fasta).collect() : Channel.value([])
49-
dict = params.dict ? Channel.fromPath(params.dict).collect() : Channel.empty()
50-
51-
// Genome version
52-
genome = params.genome ?: Channel.empty()
86+
fasta = params.fasta ? channel.fromPath(params.fasta).collect() : channel.value([])
87+
dict = params.dict ? channel.fromPath(params.dict).collect() : channel.empty()
5388

5489
// VEP cache
55-
vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([])
56-
vep_cache_unpacked = Channel.value([])
57-
90+
vep_cache = params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([])
91+
vep_cache_unpacked = channel.value([])
5892

5993
//
6094
// WORKFLOW: Run pipeline
6195
//
6296

63-
VCFTOMAF (
97+
VCFTOMAF(
6498
samplesheet,
6599
intervals,
66100
fasta,
67101
dict,
68102
liftover_chain,
69-
genome,
70103
vep_cache,
71-
vep_cache_unpacked
104+
vep_cache_unpacked,
72105
)
73106

74107
emit:
75108
multiqc_report = VCFTOMAF.out.multiqc_report // channel: /path/to/multiqc_report.html
76109
}
77-
/*
78-
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
79-
RUN MAIN WORKFLOW
80-
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
81-
*/
82-
83-
workflow {
84-
85-
main:
86-
//
87-
// SUBWORKFLOW: Run initialisation tasks
88-
//
89-
PIPELINE_INITIALISATION (
90-
params.version,
91-
params.validate_params,
92-
params.monochrome_logs,
93-
args,
94-
params.outdir,
95-
params.input,
96-
params.help,
97-
params.help_full,
98-
params.show_hidden
99-
)
100-
101-
//
102-
// WORKFLOW: Run main workflow
103-
//
104-
QBICPIPELINES_VCFTOMAF (
105-
PIPELINE_INITIALISATION.out.samplesheet
106-
)
107-
108-
//
109-
PIPELINE_COMPLETION (
110-
params.email,
111-
params.email_on_fail,
112-
params.plaintext_email,
113-
params.outdir,
114-
params.monochrome_logs,
115-
params.hook_url,
116-
QBICPIPELINES_VCFTOMAF.out.multiqc_report
117-
)
118-
}
119-
120-
/*
121-
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
122-
THE END
123-
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
124-
*/

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