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Merge pull request #69 from nvnieuwk/fix/formatting
Fix formatting issues
2 parents 91b0f8c + df86d60 commit e5c296e

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8 files changed

+21
-45
lines changed

8 files changed

+21
-45
lines changed

‎main.nf‎

Lines changed: 0 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -52,7 +52,6 @@ workflow {
5252
PIPELINE_INITIALISATION (
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params.version,
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params.validate_params,
55-
params.monochrome_logs,
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args,
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params.outdir,
5857
params.input
@@ -66,12 +65,6 @@ workflow {
6665
error "You must provide either a UCSC FASTA file (--ucsc_fasta) or a NCBI FASTA file (--ncbi_fasta)."
6766
}
6867

69-
// Use the UCSC FASTA and FAI files if provided, otherwise use the NCBI FASTA and FAI files
70-
def fasta = params.ucsc_fasta ? Channel.value([[id: 'fasta'], file(params.ucsc_fasta)]) :
71-
params.ncbi_fasta ? Channel.value([[id: 'fasta'], file(params.ncbi_fasta)]) : Channel.empty()
72-
def fai = params.ucsc_fai ? Channel.value([[id: 'fai'], file(params.ucsc_fai)]) :
73-
params.ncbi_fai ? Channel.value([[id: 'fai'], file(params.ncbi_fai)]) : Channel.empty()
74-
7568
def ucsc_fasta = params.ucsc_fasta ? Channel.value([[id: 'ucsc'], file(params.ucsc_fasta)]) : Channel.of([[id:'ucsc'], []])
7669
def ucsc_fai = params.ucsc_fai ? Channel.value([[id: 'ucsc'], file(params.ucsc_fai)]) : Channel.of([[id:'ucsc'], []])
7770
def ncbi_fasta = params.ncbi_fasta ? Channel.value([[id: 'ncbi'], file(params.ncbi_fasta)]) : Channel.of([[id:'ncbi'], []])
@@ -105,9 +98,6 @@ workflow {
10598

10699
def hpo_file = params.hpo_file ? Channel.value([[id: 'hpo'], file(params.hpo_file)]) : [[:], []]
107100

108-
def ec_gene_annotations = params.ec_gene_annotations ? params.ec_gene_annotations.tokenize(",") : []
109-
def ec_exclude_groups = params.ec_exclude_groups ? params.ec_exclude_groups.tokenize(",") : []
110-
111101
def ae_groups = params.ae_groups ? params.ae_groups.tokenize(",") : []
112102
def ae_genes_to_test = params.ae_genes_to_test ? Channel.value([[id: 'genes_to_test'], file(params.ae_genes_to_test)]) : [[:], []]
113103

@@ -123,9 +113,6 @@ workflow {
123113
// Global parameters
124114
PIPELINE_INITIALISATION.out.samplesheet, // derived from --input
125115
samplesheet_file,
126-
params.project_title,
127-
fasta,
128-
fai,
129116
ucsc_fasta,
130117
ucsc_fai,
131118
ncbi_fasta,
@@ -136,10 +123,6 @@ workflow {
136123
hpo_file,
137124
qc_vcf,
138125

139-
// Export counts parameters
140-
ec_gene_annotations,
141-
ec_exclude_groups,
142-
143126
// Aberrant expression parameters
144127
params.ae_skip,
145128
ae_groups,

‎modules/local/genecounts/summary/main.nf‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,6 @@ process GENECOUNTS_SUMMARY {
3131
template 'Summary.R'
3232

3333
stub:
34-
def prefix = task.ext.prefix ?: "${meta.id}"
3534
"""
3635
#!/usr/bin/env Rscript
3736
a <- file("sample_count_mqc.tsv", "w")

‎modules/local/outrider/summary/main.nf‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,6 @@ process OUTRIDER_SUMMARY {
3434
template 'Summary.R'
3535

3636
stub:
37-
def prefix = task.ext.prefix ?: "${meta.id}"
3837
"""
3938
#!/usr/bin/env Rscript
4039
a <- file("outrider_overview_mqc.tsv", "w")

‎subworkflows/local/aberrantexpression/main.nf‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -192,7 +192,7 @@ workflow ABERRANTEXPRESSION {
192192
// Calculate and merge the BAM stats
193193
//
194194
def external_samples = inputs_to_analyse
195-
.filter { meta, bam, _bai, gene_counts ->
195+
.filter { _meta, bam, _bai, gene_counts ->
196196
!bam && gene_counts // no BAM but a counts file
197197
}
198198
.map { meta, _bam, _bai, _gene_counts ->
@@ -218,7 +218,7 @@ workflow ABERRANTEXPRESSION {
218218
ods_unfitted ]
219219
}
220220
.combine(BAM_STATS_IDXSTATS_MERGE.out.merged_bam_stats, by: 0)
221-
.map { group, meta, ods_unfitted, bamstats ->
221+
.map { _group, meta, ods_unfitted, bamstats ->
222222
[ meta, ods_unfitted, bamstats ]
223223
}
224224

‎subworkflows/local/bam_stats_idxstats_merge/main.nf‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@ workflow BAM_STATS_IDXSTATS_MERGE {
2121
def externals_entries = externals
2222
.map { meta -> [ meta, "${meta.id}\tNA" ] }
2323

24-
def ch_bam_stats = SAMTOOLS_IDXSTATS.out.idxstats
24+
SAMTOOLS_IDXSTATS.out.idxstats
2525
// Get the total read count for each sample
2626
.map { meta, idxstats ->
2727
def split_idxstats = idxstats.splitCsv(header: false, sep: "\t")

‎subworkflows/local/mae/main.nf‎

Lines changed: 15 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -11,19 +11,20 @@ include { MULTIQC as MULTIQC_MAEQC } from '../../../modules/nf-core/multiqc
1111

1212
workflow MAE {
1313
take:
14-
input // queue channel: [ val(meta), path(vcf), path(tbi), path(bam), path(bai) ]
15-
ucsc_fasta // value channel: [ val(meta), path(ucsc_fasta) ]
16-
ucsc_fai // value channel: [ val(meta), path(ucsc_fai) ]
17-
ucsc_dict // value channel: [ val(meta), path(ucsc_dict) ]
18-
ncbi_fasta // value channel: [ val(meta), path(ncbi_fasta) ]
19-
ncbi_fai // value channel: [ val(meta), path(ncbi_fai) ]
20-
ncbi_dict // value channel: [ val(meta), path(ncbi_dict) ]
21-
gene_annotation // queue channel: [ val(meta), path(gtf) ]
22-
samplesheet // value channel: [ val(meta), path(samplesheet) ]
23-
qc_vcf // value channel: [ val(meta), path(vcf), path(tbi) ]
24-
include_groups // list : A list of groups to include in the mono allelic expression analysis
25-
ncbi2ucsc // value channel: path to the NCBI to UCSC mapping file
26-
ucsc2ncbi // value channel: path to the UCSC to NCBI mapping file
14+
input // queue channel: [ val(meta), path(vcf), path(tbi), path(bam), path(bai) ]
15+
ucsc_fasta // value channel: [ val(meta), path(ucsc_fasta) ]
16+
ucsc_fai // value channel: [ val(meta), path(ucsc_fai) ]
17+
ucsc_dict // value channel: [ val(meta), path(ucsc_dict) ]
18+
ncbi_fasta // value channel: [ val(meta), path(ncbi_fasta) ]
19+
ncbi_fai // value channel: [ val(meta), path(ncbi_fai) ]
20+
ncbi_dict // value channel: [ val(meta), path(ncbi_dict) ]
21+
gene_annotation // queue channel: [ val(meta), path(gtf) ]
22+
samplesheet // value channel: [ val(meta), path(samplesheet) ]
23+
qc_vcf // value channel: [ val(meta), path(vcf), path(tbi) ]
24+
include_groups // list : A list of groups to include in the mono allelic expression analysis
25+
include_qc_groups // list : A list of groups to include in the QC steps of the mono allelic expression analysis
26+
ncbi2ucsc // value channel: path to the NCBI to UCSC mapping file
27+
ucsc2ncbi // value channel: path to the UCSC to NCBI mapping file
2728

2829
main:
2930
def ch_versions = Channel.empty()
@@ -126,6 +127,7 @@ workflow MAE {
126127
)
127128
ch_versions = ch_versions.mix(MAE_RESULTS.out.versions.first())
128129

130+
// TODO implement mae_qc_groups logic
129131
MAEQC_DNARNADESEQ(
130132
MAE_ALLELICCOUNTS.out.csv
131133
)

‎subworkflows/local/utils_nfcore_drop_pipeline/main.nf‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,6 @@ workflow PIPELINE_INITIALISATION {
2828
take:
2929
version // boolean: Display version and exit
3030
validate_params // boolean: Boolean whether to validate parameters against the schema at runtime
31-
monochrome_logs // boolean: Do not use coloured log outputs
3231
nextflow_cli_args // array: List of positional nextflow CLI args
3332
outdir // string: The output directory where the results will be saved
3433
input // string: Path to input samplesheet
@@ -86,7 +85,7 @@ workflow PIPELINE_INITIALISATION {
8685
// Create channel from input file provided through params.input
8786
//
8887

89-
def samplesheet_list = samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")
88+
def samplesheet_list = samplesheetToList(input, "${projectDir}/assets/schema_input.json")
9089

9190
// Enforce consistent strandedness per DROP_GROUP (no mixing 'no' with 'yes'/'reverse')
9291
validateGroupStrandedness(samplesheet_list)

‎workflows/drop.nf‎

Lines changed: 2 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -29,9 +29,6 @@ workflow DROP {
2929
// Global parameters
3030
samplesheet // queue channel: samplesheet read in from --input
3131
samplesheet_file // value channel: [ val(meta), path(samplesheet) ]
32-
project_title // string: title of the project to add to the HTML file
33-
fasta // value channel: [ val(meta), path(fasta) ]
34-
fai // value channel: [ val(meta), path(fai) ]
3532
ucsc_fasta // value channel: [ val(meta), path(ucsc_fasta) ]
3633
ucsc_fai // value channel: [ val(meta), path(ucsc_fai) ]
3734
ncbi_fasta // value channel: [ val(meta), path(ncbi_fasta) ]
@@ -42,10 +39,6 @@ workflow DROP {
4239
hpo_file // value channel: [ val(meta), path(hpo_file) ]
4340
qc_vcf // value channel: [ val(meta), path(vcf), path(tbi) ]
4441

45-
// Export count parameters
46-
ec_gene_annotations // list: A list of gene annotations to export the counts of
47-
ec_exclude_groups // list: A list of groups to exclude from the counts export
48-
4942
// Aberrant expression parameters
5043
ae_skip // boolean: Skip aberrant expression analysis
5144
ae_groups // list: A list of groups to exclude from the aberrant expression analysis
@@ -191,7 +184,8 @@ workflow DROP {
191184
gene_annotation,
192185
samplesheet_file,
193186
qc_vcf,
194-
params.mae_groups.tokenize(","),
187+
mae_groups,
188+
mae_qc_groups,
195189
Channel.value(file("${projectDir}/assets/chr_NCBI_UCSC.txt", checkIfExists: true)),
196190
Channel.value(file("${projectDir}/assets/chr_UCSC_NCBI.txt", checkIfExists: true))
197191
)

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