Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
params {
// Input options
input = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
chromosome_size = null
restriction_fragments = null
save_reference = false
// Mapping
split_fastq = false
fastq_chunks_size = 20000000
save_interaction_bam = false
save_aligned_intermediates = false
bwt2_opts_end2end = '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'
bwt2_opts_trimmed = '--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'
keep_dups = false
keep_multi = false
min_mapq = 10
// Digestion Hi-C
digestion = null
ligation_site = null
restriction_site = null
digest {
'hindiii'{
restriction_site='A^AGCTT'
ligation_site='AAGCTAGCTT'
}
'mboi' {
restriction_site='^GATC'
ligation_site='GATCGATC'
}
'dpnii' {
restriction_site='^GATC'
ligation_site='GATCGATC'
}
'arima' {
restriction_site='^GATC,G^ANTC'
ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC'
}
}
min_restriction_fragment_size = 0
max_restriction_fragment_size = 0
min_insert_size = 0
max_insert_size = 0
save_pairs_intermediates = false
// Dnase Hi-C
dnase = false
min_cis_dist = 0
// Contact maps
save_raw_maps = false
bin_size = '1000000'
res_zoomify = null
hicpro_maps = false
ice_max_iter = 100
ice_filter_low_count_perc = 0.02
ice_filter_high_count_perc = 0
ice_eps = 0.1
// Downstream Analysis
res_dist_decay = '250000'
tads_caller = 'insulation'
res_tads = '40000'
res_compartments = '250000'
// Workflow
skip_maps = false
skip_balancing = false
skip_mcool = false
skip_dist_decay = false
skip_compartments = false
skip_tads = false
skip_multiqc = false
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,digest'
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Hicstuff
hicstuff_bwt2_align_opts = '--very-sensitive-local'
hicstuff_min_size = 0
hicstuff_output_contigs = 'info_contigs.txt'
hicstuff_output_frags = 'fragments_list.txt'
hicstuff_frags_plot = 'false'
hicstuff_frags_plot_path = 'frags_hist.pdf'
hicstuff_valid_pairs = 'valid.pairs'
hicstuff_valid_idx = 'valid_idx.pairs'
hicstuff_min_qual = 30
hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
hicstuff_valid_idx_filtered = 'valid_idx_filtered.pairs'
hicstuff_plot_events = 'false'
hicstuff_pie_plot = 'distrib'
hicstuff_dist_plot = 'dist'
hicstuff_centro_file = 'None' //give absolute path or 'None'
hicstuff_base = 1.1
hicstuff_distance_out_file = 'distance_law.txt'
hicstuff_rm_centro = 'None' //int or 'None'
hicstuff_distance_plot = 'false'
hicstuff_distance_out_plot = 'plot_distance_law.pdf'
hicstuff_filter_pcr_out_file = 'valid_idx_pcrfree.pairs'
filter_event = false
distance_law = false
filter_pcr = false
filter_pcr_picard = true
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
process {
//Default
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: 'copy',
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
withName: 'BOWTIE2_ALIGNMENT' {
ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}" }
ext.args = params.hicstuff_bwt2_align_opts
publishDir = [
path: { "${params.outdir}/hicstuff/reads"},
mode: 'copy'
]
}
withName: 'FRAGMENT_ENZYME' {
ext.args = { [
" -m ${params.hicstuff_min_size}",
" -c ${params.hicstuff_circular}",
" -o ${params.hicstuff_output_contigs}",
" -f ${params.hicstuff_output_frags}",
" -p ${params.hicstuff_frags_plot}",
" -g ${params.hicstuff_frags_plot_path}"
].join('').trim() }
publishDir = [
path: { "${params.outdir}/hicstuff/fragment_enzyme" },
mode: 'copy'
]
}
withName: 'BAM2PAIRS' {
ext.pairs = params.hicstuff_valid_pairs
ext.index = params.hicstuff_valid_idx
" -q ${params.hicstuff_min_qual}",
" -c ${params.hicstuff_circular}"
publishDir = [
path: { "${params.outdir}/hicstuff/pairs" },
mode: 'copy'
]
}
withName: 'FILTER_EVENT' {
ext.args = { [
" -o ${params.hicstuff_valid_idx_filtered}",
" --plot ${params.hicstuff_plot_events}",
" -d ${params.hicstuff_dist_plot}",
" -q ${params.hicstuff_pie_plot}"
].join('').trim() }
publishDir = [
path: { "${params.outdir}/hicstuff/pairs" },
mode: 'copy'
]
}
withName: 'DISTANCE_LAW' {
ext.args = { [
" -c ${params.hicstuff_centro_file}",
" -b ${params.hicstuff_base}",
" -o ${params.hicstuff_distance_out_file}",
" -u ${params.hicstuff_circular}",
" -r ${params.hicstuff_rm_centro}",
" -l ${params.hicstuff_distance_plot}",
" -d ${params.hicstuff_distance_out_plot}"
].join('').trim() }
publishDir = [
path: { "${params.outdir}/hicstuff/pairs" },
mode: 'copy'
]
}
withName: 'FILTER_PCR' {
ext.args = { [
"-o ${params.hicstuff_filter_pcr_out_file}"
].join('').trim() }
publishDir = [
path: { "${params.outdir}/hicstuff/pairs" },
mode: 'copy'
]
}
withName: 'GATK4_MARKDUPLICATES' {
ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}.bam" }
ext.args = { [
"--REMOVE_DUPLICATES true"
].join('').trim() }
publishDir = [
path: { "${params.outdir}/gatk4/bam" },
mode: 'copy'
]
}
withName: 'PICARD_MARKDUPLICATES' {
ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}" }
ext.args = { [
"--REMOVE_DUPLICATES true"
].join('').trim() }
publishDir = [
path: { "${params.outdir}/picard/bam" },
mode: 'copy'
]
}
withName: 'SAMTOOLS_SORT' {
ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}_sorted" }
ext.args = { [
""
].join('').trim() }
}
withName: 'SAMTOOLS_SORT_N' {
ext.prefix = { "${meta.id}_${meta.chunk}_${meta.mates}_nsorted" }
ext.args = { [
"-n"
].join('').trim() }
publishDir = [
path: { "${params.outdir}/gatk4/bam" },
mode: 'copy'
]
}
withName: 'SAMTOOLS_INDEX' {
ext.args = { [
""
].join('').trim() }
}
ext.args = params.hicstuff_matrix
publishDir = [
path: { "${params.outdir}/hicstuff/matrix" },
mode: 'copy'
]
}
withName: 'BUILD_MATRIX_COOL' {
ext.args = params.hicstuff_matrix
publishDir = [
path: { "${params.outdir}/hicstuff/matrix" },
mode: 'copy'
]
}
withName: 'BUILD_MATRIX_COOL_ALT' {
ext.outname = params.hicstuff_matrix
ext.bin = params.hicstuff_bin
ext.args = {"-c1 2 -p1 3 -p2 4 -c2 5"}
publishDir = [
path: { "${params.outdir}/hicstuff/matrix" },
mode: 'copy'
]
}
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
//**********************************************
// PREPARE_GENOME
withName: 'BOWTIE2_BUILD' {
publishDir = [
path: { "${params.outdir}/genome/bowtie2_index" },
mode: 'copy'
]
}
withName: 'CUSTOM_GETCHROMSIZES' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: 'copy'
]
}
withName: 'GET_RESTRICTION_FRAGMENTS' {
publishDir = [
path: { "${params.outdir}/genome" },
mode: 'copy'
]
}
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}