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Joon-KlapsJoon-Klaps
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continue at spades
1 parent 25c70fb commit 1e1db70

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+93
-98
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2 files changed

+93
-98
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‎conf/modules.config

+77-85
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@ process {
2828
// Pre-processing
2929
//
3030
withName: FASTQC_RAW {
31-
ext.args = { params.arguments_fastqc ?: '' }
31+
ext.args = params.arguments_fastqc
3232
ext.prefix = { "${meta.id}_raw" }
3333
publishDir = [
3434
path: { "${params.outdir}/preprocessing/fastqc/raw" },
@@ -39,7 +39,7 @@ process {
3939
}
4040

4141
withName: TRIMMOMATIC {
42-
ext.args = {"ILLUMINACLIP:${params.adapter_fasta}:2:30:10"}
42+
ext.args = params.arguments_trimmomatic
4343
publishDir = [
4444
[
4545
path: { "${params.outdir}/preprocessing/trimmomatic/log" },
@@ -58,7 +58,7 @@ process {
5858
}
5959

6060
withName: FASTP {
61-
ext.args = { params.arguments_fastp ?: '' }
61+
ext.args = params.arguments_fastp
6262
publishDir = [
6363
[
6464
path: { "${params.outdir}/preprocessing/fastp/report" },
@@ -90,6 +90,7 @@ process {
9090
}
9191

9292
withName: UMITOOLS_EXTRACT{
93+
ext.args = params.arguments_umitools_extract
9394
publishDir = [
9495
[
9596
path: { "${params.outdir}/preprocessing/umi/umitools/log" },
@@ -109,7 +110,7 @@ process {
109110

110111

111112
withName: HUMID {
112-
ext.args = { params.arguments_humid ?: '' }
113+
ext.args = '-s' + (params.arguments_humid?: '')
113114
publishDir = [
114115
[
115116
path: { "${params.outdir}/preprocessing/umi/humid/log" },
@@ -135,7 +136,7 @@ process {
135136
}
136137

137138
withName: BBMAP_BBDUK {
138-
ext.args = { params.arguments_bbduk ?: '' }
139+
ext.args = params.arguments_bbduk
139140
publishDir = [
140141
[
141142
path: { "${params.outdir}/preprocessing/bbduk/log" },
@@ -154,7 +155,7 @@ process {
154155
}
155156

156157
withName: PRINSEQ_READS {
157-
ext.args = { params.arguments_prinseq_reads ?: '' }
158+
ext.args = '-out_gz' + (params.arguments_prinseq_reads?: '')
158159
publishDir = [
159160
[
160161
path: { "${params.outdir}/preprocessing/prinseq" },
@@ -173,7 +174,7 @@ process {
173174
}
174175

175176
withName: FASTQC_TRIM {
176-
ext.args = { params.arguments_fastqc ?: '' }
177+
ext.args = params.arguments_fastqc
177178
ext.prefix = { "${meta.id}_trim" }
178179
publishDir = [
179180
path: { "${params.outdir}/preprocessing/fastqc/trim" },
@@ -194,7 +195,8 @@ process {
194195
}
195196

196197
withName: KRAKEN2_HOST_REMOVE {
197-
memory = { 200.GB * task.attempt }
198+
memory = { 200.GB * task.attempt }
199+
ext.args = params.arguments_kraken2_host
198200
ext.prefix = { "${meta.id}_kraken2_host" }
199201
publishDir = [
200202
[
@@ -214,7 +216,7 @@ process {
214216
}
215217

216218
withName: FASTQC_HOST {
217-
ext.args = { params.arguments_fastqc ?: '' }
219+
ext.args = params.arguments_fastqc
218220
ext.prefix = { "${meta.id}_host" }
219221
publishDir = [
220222
path: { "${params.outdir}/preprocessing/fastqc/host" },
@@ -251,16 +253,16 @@ process {
251253
]
252254
}
253255

254-
withName: SEQKIT_REPLACE{
255-
ext.args = { params.arguments_seqkit_replace ?: '' }
256-
ext.suffix= 'fasta'
256+
withName: SEQKIT_REPLACE {
257+
ext.args = '-p "[\\|\\/\\\\\\]" -r "-"'
258+
ext.suffix = 'fasta'
257259
publishDir = [
258260
enabled: false,
259261
]
260262
}
261263

262-
withName: BLAST_MAKEBLASTDB{
263-
ext.args = { params.arguments_blast_makeblastdb ?: '' }
264+
withName: BLAST_MAKEBLASTDB {
265+
ext.args = params.arguments_blast_makeblastdb
264266
publishDir = [
265267
path: { "${params.outdir}/databases/" },
266268
mode: params.publish_dir_mode,
@@ -271,84 +273,74 @@ process {
271273
]
272274
}
273275

274-
//
275-
// Taxonomic classification
276-
//
277-
if (!params.skip_read_classification){
278-
279-
withName: KRAKEN2_KRAKEN2 {
280-
ext.prefix = { "${meta.id}_kraken2" }
281-
ext.args = [
282-
params.kraken2_save_minimizers ? { "--report-minimizer-data" } : "",
283-
].join(' ').trim()
284-
publishDir = [
285-
path: { "${params.outdir}/metagenomic_diversity/kraken2/" },
286-
mode: params.publish_dir_mode,
287-
pattern: '*.{txt,fastq.gz}',
288-
saveAs: { filename -> params.prefix || params.global_prefix ? "${params.global_prefix}-$filename" : filename }
289-
]
290-
}
276+
withName: KRAKEN2_KRAKEN2 {
277+
ext.prefix = { "${meta.id}_kraken2" }
278+
ext.args = params.arguments_kraken
279+
publishDir = [
280+
path: { "${params.outdir}/metagenomic_diversity/kraken2/" },
281+
mode: params.publish_dir_mode,
282+
pattern: '*.{txt,fastq.gz}',
283+
saveAs: { filename -> params.prefix || params.global_prefix ? "${params.global_prefix}-$filename" : filename }
284+
]
285+
}
291286

292-
withName: BRACKEN_BRACKEN {
293-
ext.prefix = { "${meta.id}_bracken" }
294-
publishDir = [
295-
path: { "${params.outdir}/metagenomic_diversity/bracken/" },
296-
mode: params.publish_dir_mode,
297-
pattern: '*.tsv',
298-
saveAs: { filename -> params.prefix || params.global_prefix ? "${params.global_prefix}-$filename" : filename }
299-
]
300-
}
287+
withName: BRACKEN_BRACKEN {
288+
ext.prefix = { "${meta.id}_bracken" }
289+
publishDir = [
290+
path: { "${params.outdir}/metagenomic_diversity/bracken/" },
291+
mode: params.publish_dir_mode,
292+
pattern: '*.tsv',
293+
saveAs: { filename -> params.prefix || params.global_prefix ? "${params.global_prefix}-$filename" : filename }
294+
]
295+
}
301296

302-
withName: KRAKENTOOLS_KREPORT2KRONA {
303-
publishDir = [
304-
enabled: false,
305-
]
306-
}
297+
withName: KRAKENTOOLS_KREPORT2KRONA {
298+
publishDir = [
299+
enabled: false,
300+
]
301+
}
307302

308-
withName: KAIJU_KAIJU {
309-
ext.args = { params.arguments_kaiju ?: '' }
310-
publishDir = [
311-
path: { "${params.outdir}/metagenomic_diversity/kaiju/" },
312-
mode: params.publish_dir_mode,
313-
pattern: '*.tsv',
314-
saveAs: { filename -> params.prefix || params.global_prefix ? "${params.global_prefix}-$filename" : filename }
315-
]
316-
}
303+
withName: KAIJU_KAIJU {
304+
ext.args = params.arguments_kaiju
305+
publishDir = [
306+
path: { "${params.outdir}/metagenomic_diversity/kaiju/" },
307+
mode: params.publish_dir_mode,
308+
pattern: '*.tsv',
309+
saveAs: { filename -> params.prefix || params.global_prefix ? "${params.global_prefix}-$filename" : filename }
310+
]
311+
}
317312

318-
withName: KAIJU_KAIJU2TABLE {
319-
ext.args = { [
320-
params.arguments_kaiju2table ?: '',
321-
"-l ${params.kaiju_taxon_rank}"
322-
].join(' ').trim() }
323-
publishDir = [
324-
path: { "${params.outdir}/metagenomic_diversity/kaiju/" },
325-
mode: params.publish_dir_mode,
326-
pattern: '*.{txt}',
327-
saveAs: { filename -> params.prefix || params.global_prefix ? "${params.global_prefix}-$filename" : filename }
328-
]
329-
}
313+
withName: KAIJU_KAIJU2TABLE {
314+
ext.args = params.arguments_kaiju2table
315+
publishDir = [
316+
path: { "${params.outdir}/metagenomic_diversity/kaiju/" },
317+
mode: params.publish_dir_mode,
318+
pattern: '*.{txt}',
319+
saveAs: { filename -> params.prefix || params.global_prefix ? "${params.global_prefix}-$filename" : filename }
320+
]
321+
}
330322

331-
withName: KAIJU_KAIJU2KRONA {
332-
ext.prefix = { "${meta.id}_kaiju" }
333-
ext.args = '-v -u'
334-
publishDir = [
335-
enabled: false
336-
]
337-
}
323+
withName: KAIJU_KAIJU2KRONA {
324+
ext.prefix = { "${meta.id}_kaiju" }
325+
ext.args = params.arguments_kaiju2krona
326+
publishDir = [
327+
enabled: false
328+
]
329+
}
338330

339-
withName: KRONA_CLEANUP {
340-
publishDir = [
341-
enabled: false
342-
]
343-
}
331+
withName: KRONA_CLEANUP {
332+
publishDir = [
333+
enabled: false
334+
]
335+
}
344336

345-
withName: KRONA_KTIMPORTTEXT {
346-
publishDir = [
347-
path: { "${params.outdir}/metagenomic_diversity/krona/" },
348-
mode: params.publish_dir_mode,
349-
pattern: '*.{html}'
350-
]
351-
}
337+
withName: KRONA_KTIMPORTTEXT {
338+
ext.args = params.arguments_krona
339+
publishDir = [
340+
path: { "${params.outdir}/metagenomic_diversity/krona/" },
341+
mode: params.publish_dir_mode,
342+
pattern: '*.{html}'
343+
]
352344
}
353345

354346
//

‎nextflow.config

+16-13
Original file line numberDiff line numberDiff line change
@@ -25,8 +25,6 @@ params {
2525
umi_discard_read = 0 // 0 = no discard
2626
umi_separator = ":"
2727
umi_deduplicate = 'read'
28-
humid_mismatches = 1
29-
humid_strategy = 'directional' // directional vs cluster
3028
umitools_dedup_strategy = 'cluster'
3129

3230
// > Trim
@@ -36,8 +34,6 @@ params {
3634
save_trimmed_fail = false
3735
save_merged = false
3836
min_trimmed_reads = 1
39-
fastp_deduplicate = false
40-
fastp_dedup_accuracy = null
4137

4238
// > complexity
4339
skip_complexity_filtering = true
@@ -63,7 +59,6 @@ params {
6359
bracken_db = "https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20230314.tar.gz"
6460
// > Kaiju
6561
kaiju_db = "https://kaiju-idx.s3.eu-central-1.amazonaws.com/2023/kaiju_db_rvdb_2023-05-26.tgz"
66-
kaiju_taxon_rank = 'species'
6762

6863
// ASSEMBLY
6964
skip_assembly = false
@@ -194,10 +189,23 @@ params {
194189
validate_params = true
195190

196191
// Module specific arguments
192+
arguments_fastqc = '--quiet'
197193
arguments_fastp = '--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50'
198-
arguments_humid = '-a -s'
194+
arguments_trimmomatic = "ILLUMINACLIP:${adapter_fasta}:2:30:10"
195+
arguments_umitools_extract = null
196+
// leave empty for directional strategy add -x for cluster strategy
197+
arguments_humid = '-a -m 1'
199198
arguments_bbduk = 'entropy=0.3 entropywindow=50 entropymask=f'
200-
arguments_prinseq_reads = '-out_gz'
199+
arguments_prinseq_reads = null
200+
arguments_kraken_host = null
201+
arguments_blast_makeblastdb = '-dbtype nucl'
202+
203+
arguments_kraken = '--report-minimizer-data'
204+
arguments_kaiju = '-v'
205+
arguments_kaiju2table = '-e -l species'
206+
arguments_kaiju2krona = '-v -u'
207+
arguments_krona = null
208+
201209
arguments_spades = '' // Leave empty by default, mode is handled separately
202210
arguments_sspace_basic = '-x 1 -o 15 -r 0.75'
203211
arguments_bowtie2_align = '--local --very-sensitive-local --seed 1'
@@ -214,17 +222,12 @@ params {
214222
arguments_mmseqs_cluster = '--min-seq-id 0.85 -c 0.700 --cov-mode 2 -s 7'
215223
arguments_vrhyme = '--mems 50'
216224
arguments_mash_sketch = '-i'
217-
arguments_fastqc = '--quiet'
218-
arguments_kaiju = '-v'
219-
arguments_kaiju2table = '-e'
220-
arguments_kaiju2krona = '-v -u'
221225
arguments_quast = '--min-contig 0'
222226
arguments_bwamem2 = '-R "@RG\\tID:{meta.id}\\tSM:{meta.sample}\\tPL:ILLUMINA"'
223227
arguments_picard_metrics = '--VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
224228
arguments_bcftools_norm = '--do-not-normalize --output-type z --multiallelics -any'
225229
arguments_bedtools_merge = ''
226-
arguments_seqkit_replace = '-p "[\\|\\/\\\\\\]" -r "-"'
227-
arguments_blast_makeblastdb = '-dbtype nucl'
230+
228231
arguments_cdhit = "-d 50 -mask rRyYkKsSwWmMbBdDhHvVnN"
229232
arguments_vsearch = "--strand both --iddef 0 --no_progress --qmask none"
230233
arguments_blastn = '-max_target_seqs 5 -outfmt "6 qseqid sseqid stitle pident qlen slen length mismatch gapopen qstart qend sstart send evalue bitscore"'

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