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janaHoffmann1janaHoffmann1
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fix lint and pre-commit error
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Lines changed: 152 additions & 133 deletions

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‎README.md‎

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Original file line numberDiff line numberDiff line change
@@ -131,6 +131,7 @@ Helpful contributors:
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- [Sven Fillinger](https://github.com/sven1103)
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- [Kevin Menden](https://github.com/KevinMenden)
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- [Julia Graf](https://github.com/JuliaGraf)
134+
- [Jana Hoffmann](https://github.com/janaHoffmann1)
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## Contributions and Support
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‎assets/multiqc_config.yml‎

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@@ -162,7 +162,7 @@ sp:
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fn: "epicore_length_distribution.html"
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epicore_intensity_histogram:
164164
fn: "epicore_intensity_histogram.html"
165-
165+
166166
### Define the order of sections
167167
#module_order:
168168
# - custom_content

‎conf/modules.config‎

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Original file line numberDiff line numberDiff line change
@@ -436,24 +436,24 @@ process {
436436
publishDir = [
437437
path: {"${params.outdir}"},
438438
mode: params.publish_dir_mode,
439-
pattern: "*.tsv",
439+
pattern: "*.tsv",
440440
enabled: !params.epicore
441441
]
442442
}
443-
443+
444444
withName: 'EPICORE' {saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
445445
ext.args = [
446-
"--seq_column ${params.seq_column}",
446+
"--seq_column ${params.seq_column}",
447447
"--protacc_column ${params.protacc_column}",
448-
params.intensity_column ? "--intensity_column ${params.intensity_column}" : "--intensity_column ''",
449-
params.start_column ? "--start_column ${params.start_column}" : "--start_column ''",
450-
params.end_column ? "--end_column ${params.end_column}" : "--end_column ''",
451-
params.mod_pattern ? "--mod_pattern ${params.mod_pattern}" : "--mod_pattern ''",
452-
"--delimiter ${params.delimiter}",
453-
"--min_overlap ${params.min_overlap}",
448+
params.intensity_column ? "--intensity_column ${params.intensity_column}" : "--intensity_column ''",
449+
params.start_column ? "--start_column ${params.start_column}" : "--start_column ''",
450+
params.end_column ? "--end_column ${params.end_column}" : "--end_column ''",
451+
params.mod_pattern ? "--mod_pattern ${params.mod_pattern}" : "--mod_pattern ''",
452+
"--delimiter ${params.delimiter}",
453+
"--min_overlap ${params.min_overlap}",
454454
"--max_step_size ${params.max_step_size}",
455455
"--min_epi_length ${params.min_epi_length}"
456-
].join(' ').trim()
456+
].join(' ').trim()
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publishDir = [
458458
path: {"${params.outdir}"},
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mode: params.publish_dir_mode,

‎conf/test_epicore.config‎

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Original file line numberDiff line numberDiff line change
@@ -31,11 +31,11 @@ params {
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seq_column = 'sequence'
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protacc_column = 'accessions'
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intensity_column = false
34-
start_column = false
34+
start_column = false
3535
end_column = false
3636
mod_pattern = false
3737
delimiter = '";"'
3838
min_overlap = '11'
3939
max_step_size = '5'
4040
min_epi_length = '11'
41-
}
41+
}

‎modules/local/epicore.nf‎

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Original file line numberDiff line numberDiff line change
@@ -1,56 +1,55 @@
11
process EPICORE {
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tag "$meta.id"
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label 'process_high'
4-
5-
conda "bioconda::epicore=0.1.5"
6-
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/epicore:0.1.5--pyhdfd78af_0' :
8-
'biocontainers/epicore:0.1.5--pyhdfd78af_0' }"
9-
10-
input:
11-
tuple val(meta_fasta), path(fasta)
12-
path(quantification_tsv)
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path(general_stats)
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val(meta)
15-
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output:
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path "*_general_stats.csv", emit: stats
18-
path "${meta.id}.csv", emit: final_epicore_csv
19-
path "epicore_length_distribution.html", emit: length_dist
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path "epicore_intensity_histogram.html", emit: intensity_hist
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path "versions.yml", emit: versions
22-
23-
script:
24-
def args = task.ext.args ?: ''
25-
def prefix = task.ext.prefix ?: "${meta.id}"
26-
"""#!/bin/bash
27-
28-
epicore --reference_proteome $fasta --out_dir . generate-epicore-csv $args --evidence_file $quantification_tsv --html
29-
30-
mv pep_cores_mapping.csv ${prefix}.csv
31-
mv length_distributions.html epicore_length_distribution.html
32-
mv epitope_intensity_hist.html epicore_intensity_histogram.html
33-
34-
wc -l < epitopes.csv | awk '{print \$1 - 1}' > epicores.txt
35-
36-
awk 'NR==1 {print \$0 ",# Epicores"; next} NR==2 {getline extra < "epicores.txt"; print \$0 "," extra}' $general_stats > _modified_$general_stats
37-
cat <<-END_VERSIONS > versions.yml
38-
"${task.process}":
39-
epicore: \$(epicore --version | grep 'epicore' | cut -d ' ' -f3)
40-
END_VERSIONS
41-
"""
42-
43-
stub:
44-
def args = task.ext.args ?: ''
45-
def prefix = task.ext.prefix ?: "${meta.id}"
46-
"""
47-
touch ${prefix}_general_stats.csv
48-
touch ${meta.id}_epicore.csv
49-
touch length_distributions.html
50-
touch epitope_intensity_hist.html
51-
cat <<-END_VERSIONS > versions.yml
52-
"${task.process}":
53-
epicore: \$(epicore --version | grep 'epicore' | cut -d ' ' -f3)
54-
END_VERSIONS
55-
"""
56-
}
2+
tag "$meta.id"
3+
label 'process_high'
4+
5+
conda "bioconda::epicore=0.1.5"
6+
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7+
'https://depot.galaxyproject.org/singularity/epicore:0.1.5--pyhdfd78af_0' :
8+
'biocontainers/epicore:0.1.5--pyhdfd78af_0' }"
9+
10+
input:
11+
tuple val(meta_fasta), path(fasta)
12+
path(quantification_tsv)
13+
path(general_stats)
14+
val(meta)
15+
16+
output:
17+
path "*_general_stats.csv", emit: stats
18+
path "${meta.id}.csv", emit: final_epicore_tsv
19+
path "epicore_length_distribution.html", emit: length_dist
20+
path "epicore_intensity_histogram.html", emit: intensity_hist
21+
path "versions.yml", emit: versions
22+
23+
script:
24+
def args = task.ext.args ?: ''
25+
def prefix = task.ext.prefix ?: "${meta.id}"
26+
"""#!/bin/bash
27+
28+
epicore --reference_proteome $fasta --out_dir . generate-epicore-csv $args --evidence_file $quantification_tsv --html
29+
30+
mv pep_cores_mapping.csv ${prefix}.csv
31+
mv length_distributions.html epicore_length_distribution.html
32+
mv epitope_intensity_hist.html epicore_intensity_histogram.html
33+
34+
wc -l < epitopes.csv | awk '{print \$1 - 1}' > epicores.txt
35+
36+
awk 'NR==1 {print \$0 ",# Epicores"; next} NR==2 {getline extra < "epicores.txt"; print \$0 "," extra}' $general_stats > _modified_$general_stats
37+
cat <<-END_VERSIONS > versions.yml
38+
"${task.process}":
39+
epicore: \$(epicore --version | grep 'epicore' | cut -d ' ' -f3)
40+
"""
41+
42+
stub:
43+
def args = task.ext.args ?: ''
44+
def prefix = task.ext.prefix ?: "${meta.id}"
45+
"""
46+
touch ${prefix}_general_stats.csv
47+
touch ${meta.id}_epicore.csv
48+
touch length_distributions.html
49+
touch epitope_intensity_hist.html
50+
cat <<-END_VERSIONS > versions.yml
51+
"${task.process}":
52+
epicore: \$(epicore --version | grep 'epicore' | cut -d ' ' -f3)
53+
END_VERSIONS
54+
"""
55+
}

‎nextflow.config‎

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Original file line numberDiff line numberDiff line change
@@ -76,13 +76,13 @@ params {
7676
quantification_mapping_tolerance = 0
7777

7878
// Epicore settings
79-
seq_column = 'sequence'
80-
protacc_column = 'accessions'
81-
intensity_column = 'intensity_cf'
82-
start_column = false
83-
end_column = false
84-
mod_pattern = false
85-
delimiter = '";"'
79+
seq_column = ''
80+
protacc_column = ''
81+
intensity_column = ''
82+
start_column = ''
83+
end_column = ''
84+
mod_pattern = ''
85+
delimiter = ''
8686
min_overlap = '11'
8787
max_step_size = '5'
8888
min_epi_length = '11'
@@ -338,6 +338,14 @@ manifest {
338338
github: '@JuliaGraf',
339339
contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
340340
orcid: ''
341+
],
342+
[
343+
name: 'Jana Hoffmann',
344+
affiliation: '',
345+
email: '',
346+
github: '@janaHoffmann1',
347+
contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
348+
orcid: ''
341349
]
342350
]
343351
homePage = 'https://github.com/nf-core/mhcquant'

‎nextflow_schema.json‎

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Original file line numberDiff line numberDiff line change
@@ -424,74 +424,82 @@
424424
"fa_icon": "fas fa-tags",
425425
"description": "Create tsv files containing information about the MS2 ion annotations after processing.",
426426
"help_text": "The resulting tsv files should aid in spectrum validation downstream analyses"
427+
}
428+
}
429+
},
430+
"epicore_options": {
431+
"title": "Epicore Options",
432+
"type": "object",
433+
"fa_icon": "fa-solid fa-stairs",
434+
"description": "",
435+
"default": "",
436+
"properties": {
437+
"epicore": {
438+
"type": "boolean",
439+
"default": false,
440+
"fa_icon": "fa-solid fa-stairs",
441+
"description": "Compute core epitopes from overlapping peptides."
427442
},
428-
"epicore" : {
429-
"type": "boolean",
430-
"default": false,
431-
"fa_icon": "fas fa-layer-group",
432-
"description": "Compute core epitopes from overlapping peptides."
433-
},
434-
"seq_column" : {
435-
"type": "string",
443+
"seq_column": {
444+
"type": "string",
436445
"default": "",
437-
"fa_icon": "fas fa-dna",
446+
"fa_icon": "fa-solid fa-table",
438447
"description": "Specify the column containing the peptide sequence information."
439448
},
440-
"protacc_column" : {
441-
"type" : "string",
442-
"default": "",
443-
"hidden": true,
449+
"protacc_column": {
450+
"type": "string",
451+
"default": "",
452+
"fa_icon": "fa-solid fa-table",
444453
"description": "Specify the column containing the protein accessions of the peptide."
445-
},
446-
"start_column" : {
447-
"type" : "string",
448-
"default" : "",
449-
"hidden": true,
450-
"decsription": "Specify the column containing the start prosition of the peptide in the proetin sequence."
451-
},
452-
"end_column" : {
453-
"type" : "string",
454-
"default" : "",
455-
"hidden": true,
456-
"decsription": "Specify the column containing the end prosition of the peptide in the proetin sequence."
457-
},
458-
"intensity_column" : {
459-
"type" : "string",
460-
"default" : "",
461-
"hidden" : true,
462-
"description" :"Specify the column containing the end prosition of the peptide in the proetin sequence."
463-
},
454+
},
455+
"start_column": {
456+
"type": "string",
457+
"default": "",
458+
"fa_icon": "fa-solid fa-table",
459+
"description": "Specify the column containing the start position of the peptide in the protein sequence."
460+
},
461+
"end_column": {
462+
"type": "string",
463+
"default": "",
464+
"fa_icon": "fa-solid fa-table",
465+
"description": "Specify the column containing the end position of the peptide in the protein sequence."
466+
},
467+
"intensity_column": {
468+
"type": "string",
469+
"default": "",
470+
"fa_icon": "fa-solid fa-table",
471+
"description": "Specify the column containing the intensity of the peptide."
472+
},
464473
"mod_pattern": {
465-
"type" : "string",
466-
"default" : "",
467-
"hidden" : true,
468-
"description" :"Specify the delimiter separating the peptide sequence from modifications."
474+
"type": "string",
475+
"default": "",
476+
"fa_icon": "fa-solid fa-hashtag",
477+
"description": "Specify the delimiter separating the peptide sequence from modifications."
469478
},
470479
"delimiter": {
471-
"type" : "string",
472-
"default" : "",
473-
"hidden" : true,
474-
"description" :"Specify the delimiter separating multiple entries in one cell."
480+
"type": "string",
481+
"default": "",
482+
"fa_icon": "fa-solid fa-minus",
483+
"description": "Specify the delimiter separating multiple entries in one cell."
475484
},
476485
"min_overlap": {
477-
"type" : "string",
478-
"default" : "",
479-
"hidden" : true,
480-
"description" :"Specify the minimal overlap of two peptides so they are grouped together."
486+
"type": "string",
487+
"default": "11",
488+
"fa_icon": "fas fa-filter",
489+
"description": "Specify the minimal overlap of two peptides so they are grouped together."
481490
},
482491
"max_step_size": {
483-
"type" : "string",
484-
"default" : "",
485-
"hidden" : true,
486-
"description" :"Specify the maximal difference between the start position of two peptides so they are still grouped together."
492+
"type": "string",
493+
"default": "5",
494+
"fa_icon": "fas fa-filter",
495+
"description": "Specify the maximal difference between the start position of two peptides so they are still grouped together."
487496
},
488497
"min_epi_length": {
489-
"type" : "string",
490-
"default" : "",
491-
"hidden" : true,
492-
"description" :"Specify the minimal length of an core epitope."
498+
"type": "string",
499+
"default": "11",
500+
"fa_icon": "fas fa-filter",
501+
"description": "Specify the minimal length of an core epitope."
493502
}
494-
495503
}
496504
},
497505
"institutional_config_options": {
@@ -662,6 +670,9 @@
662670
{
663671
"$ref": "#/$defs/post_processing"
664672
},
673+
{
674+
"$ref": "#/$defs/epicore_options"
675+
},
665676
{
666677
"$ref": "#/$defs/institutional_config_options"
667678
},

‎workflows/mhcquant.nf‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -189,24 +189,24 @@ workflow MHCQUANT {
189189
// Process the tsv file to facilitate visualization with MultiQC
190190
SUMMARIZE_RESULTS(OPENMS_TEXTEXPORTER.out.tsv)
191191
ch_versions = ch_versions.mix(SUMMARIZE_RESULTS.out.versions)
192-
192+
193193
//
194194
// EPICORE
195-
//
195+
//
196196
if (params.epicore) {
197197
EPICORE(ch_fasta, SUMMARIZE_RESULTS.out.final_tsv, SUMMARIZE_RESULTS.out.stats, SUMMARIZE_RESULTS.out.meta_out)
198198

199199
ch_versions = ch_versions.mix(EPICORE.out.versions)
200-
200+
201201
ch_multiqc_files = ch_multiqc_files.mix(
202202
SUMMARIZE_RESULTS.out.hist_mz,
203203
SUMMARIZE_RESULTS.out.hist_rt,
204204
SUMMARIZE_RESULTS.out.hist_scores,
205205
SUMMARIZE_RESULTS.out.xcorr,
206206
SUMMARIZE_RESULTS.out.lengths,
207207
SUMMARIZE_RESULTS.out.intensities,
208-
EPICORE.out.stats,
209-
EPICORE.out.length_dist,
208+
EPICORE.out.stats,
209+
EPICORE.out.length_dist,
210210
EPICORE.out.intensity_hist
211211
)
212212
} else {

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