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This file
Number 2.11
Position 11 of 21
Type YAML
Size 6 KB
Lines 233 scripts/config/pipelines/ sarek.yaml
YAML · 233 lines · 6 KB
11
releases
:
"https://github.com/nf-core/sarek/releases"
12
13 data_types :
14 - WGS
15 - WES
16 - whole genome sequencing
17 - whole exome sequencing
18 - tumor-normal
19 - germline
20 - somatic
21
22 detection_hints :
23 filename :
24 - tumor
25 - normal
26 - germline
27 - wgs
28 - wes
29 - exome
30 - dna
31 - variant
32 directory :
33 - variant
34 - wgs
35 - wes
36 - exome
37 - germline
38 - somatic
39
40 samplesheet :
41 input_types :
42 - fastq
43 - bam
44 - cram
45
46 columns :
47 - name : patient
48 required : true
49 type : string
50 inference : filename
51 description : "Patient/subject identifier for grouping samples"
52
53 - name : sample
54 required : true
55 type : string
56 inference : filename
57 description : "Sample identifier (e.g., tumor, normal)"
58
59 - name : lane
60 required : false
61 type : string
62 default : "L001"
63 inference : filename
64 description : "Sequencing lane"
65
66 - name : fastq_1
67 required : true
68 type : path
69 inference : auto
70 condition : "input_type == 'fastq'"
71 description : "Absolute path to R1 FASTQ"
72
73 - name : fastq_2
74 required : false
75 type : path
76 inference : auto
77 condition : "input_type == 'fastq'"
78 description : "Absolute path to R2 FASTQ"
79
80 - name : bam
81 required : true
82 type : path
83 inference : auto
84 condition : "input_type in ['bam', 'cram']"
85 description : "Absolute path to BAM/CRAM file"
86
87 - name : bai
88 required : true
89 type : path
90 inference : auto
91 condition : "input_type in ['bam', 'cram']"
92 description : "Absolute path to BAM/CRAM index"
93
94 - name : status
95 required : false
96 type : integer
97 allowed :
98 - 0
99 - 1
100 default : 0
101 inference : filename
102 description : "0=normal, 1=tumor (critical for somatic calling)"
103
104 decision_points :
105 - parameter : genome
106 prompt : "Which reference genome should be used?"
107 options :
108 - value : GRCh38
109 label : "Human GRCh38/hg38 (recommended)"
110 description : "Latest human reference with most annotation support"
111 - value : GRCh37
112 label : "Human GRCh37/hg19 (legacy)"
113 description : "For compatibility with older datasets"
114 - value : mm10
115 label : "Mouse mm10"
116 description : "Mouse reference genome"
117 default : GRCh38
118 recommendation : "Default to GRCh38 for human data"
119
120 - parameter : tools
121 prompt : "What type of variant calling do you need?"
122 options :
123 - value : "haplotypecaller,snpeff"
124 label : "Germline variants (single samples)"
125 description : "For finding inherited variants in normal samples"
126 condition : "no tumor samples detected"
127 - value : "mutect2,strelka,snpeff"
128 label : "Somatic variants (tumor-normal pairs)"
129 description : "For finding cancer mutations with matched normal"
130 condition : "tumor-normal pairs detected"
131 - value : "haplotypecaller,deepvariant,snpeff"
132 label : "Germline with DeepVariant"
133 description : "Higher accuracy germline calling (requires GPU)"
134 - value : "mutect2,manta,snpeff"
135 label : "Somatic with structural variants"
136 description : "Comprehensive tumor analysis including SVs"
137 default : "haplotypecaller,snpeff"
138 recommendation : "Use somatic tools if tumor/normal pairs detected, otherwise germline"
139
140 - parameter : wes
141 prompt : "Is this whole exome sequencing (WES) data?"
142 options :
143 - value : "false"
144 label : "No - Whole Genome Sequencing (WGS)"
145 description : "Full genome coverage"
146 - value : "true"
147 label : "Yes - Whole Exome Sequencing (WES)"
148 description : "Requires --intervals BED file"
149 default : "false"
150 recommendation : "If WES, user must provide intervals BED file"
151
152 test_profile :
153 command : "nextflow run nf-core/sarek -r 3.7.1 -profile test,docker --outdir test_sarek"
154 duration : "20 minutes"
155 success_indicators :
156 - "test_sarek/multiqc/multiqc_report.html"
157 log_pattern : "Pipeline completed successfully"
158
159 run_command :
160 template : |
161 nextflow run nf-core/sarek \
162 -r 3.7.1 \
163 -profile docker \
164 --input {samplesheet} \
165 --outdir {outdir} \
166 --genome {genome} \
167 --tools {tools} \
168 -resume
169
170 wes_template : |
171 nextflow run nf-core/sarek \
172 -r 3.7.1 \
173 -profile docker \
174 --input {samplesheet} \
175 --outdir {outdir} \
176 --genome {genome} \
177 --tools {tools} \
178 --wes \
179 --intervals {intervals} \
180 -resume
181
182 outputs :
183 primary :
184 - path : "preprocessing/recalibrated/*.recal.bam"
185 description : "Analysis-ready BAM files"
186 - path : "variant_calling/*/*.vcf.gz"
187 description : "Variant call files"
188 - path : "annotation/snpeff/*.ann.vcf.gz"
189 description : "Annotated variants"
190
191 validation :
192 - file : "multiqc/multiqc_report.html"
193 check : exists
194 description : "QC report must exist"
195 - file : "preprocessing/recalibrated"
196 check : exists
197 description : "Recalibrated BAMs directory"
198
199 resources :
200 min_memory : "16.GB"
201 recommended_memory : "64.GB"
202 wgs_memory : "128.GB"
203 min_cpus : 4
204 recommended_cpus : 16
205 disk_space : "500.GB"
206
207 troubleshooting :
208 - error : "BQSR fails"
209 fix : "Check known sites available for genome. Skip with --skip_bqsr for non-standard references"
210 - error : "Mutect2 no variants"
211 fix : "Verify tumor/normal pairing in samplesheet (check status column: 0=normal, 1=tumor)"
212 - error : "Out of memory"
213 fix : "--max_memory '128.GB' for WGS data"
214 - error : "DeepVariant GPU issues"
215 fix : "Ensure NVIDIA Docker runtime configured, or use CPU mode"
216
217 tumor_normal_keywords :
218 tumor :
219 - tumor
220 - tumour
221 - met
222 - metastasis
223 - primary
224 - cancer
225 - malignant
226 normal :
227 - normal
228 - germline
229 - blood
230 - pbmc
231 - control
232 - healthy
233 - matched