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1 # CPIPES (CFSAN PIPELINES)
2
3 ## The modular pipeline repository at CFSAN, FDA
4
5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
7
8 ---
9
10 ### **centriflaken_hy**
11
12 ---
13 `centriflaken_hy` is a variant of the original `centriflaken` pipeline but for Illumina short reads either single-end or paired-end.
14
15 #### Workflow Usage
16
17 ```bash
18 module load cpipes/0.2.0
19
20 cpipes --pipeline centriflaken_hy [options]
21 ```
22
23 Example: Run the default `centriflaken_hy` pipeline with taxa of interest as *E. coli*.
24
25 ```bash
26 cd /hpc/scratch/$USER
27 mkdir nf-cpipes
28 cd nf-cpipes
29 cpipes --pipeline centriflaken_hy --input /path/to/illumina/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov'
30 ```
31
32 Example: Run the `centriflaken_hy` pipeline with taxa of interest as *Salmonella*. In this mode, `SerotypeFinder` tool will be replaced with `SeqSero2` tool.
33
34 ```bash
35 cd /hpc/scratch/$USER
36 mkdir nf-cpipes
37 cd nf-cpipes
38 cpipes --pipeline centriflaken_hy --centrifuge_extract_bug 'Salmonella' --input /path/to/illumina/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov'
39 ```
40
41 #### `centriflaken_hy` Help
42
43 ```text
44 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help
45 N E X T F L O W ~ version 21.12.1-edge
46 Launching `/nfs/software/apps/cpipes/0.2.1/cpipes` [wise_noyce] - revision: 72db279311
47 ================================================================================
48 (o)
49 ___ _ __ _ _ __ ___ ___
50 / __|| '_ \ | || '_ \ / _ \/ __|
51 | (__ | |_) || || |_) || __/\__ \
52 \___|| .__/ |_|| .__/ \___||___/
53 | | | |
54 |_| |_|
55 --------------------------------------------------------------------------------
56 A collection of modular pipelines at CFSAN, FDA.
57 --------------------------------------------------------------------------------
58 Name : CPIPES
59 Author : Kranti.Konganti@fda.hhs.gov
60 Version : 0.2.1
61 Center : CFSAN, FDA.
62 ================================================================================
63
64 Workflow : centriflaken_hy
65
66 Author : Kranti.Konganti@fda.hhs.gov
67
68 Version : 0.2.0
69
70
71 Usage : cpipes --pipeline centriflaken_hy [options]
72
73
74 Required :
75
76 --input : Absolute path to directory containing FASTQ
77 files. The directory should contain only
78 FASTQ files as all the files within the
79 mentioned directory will be read. Ex: --
80 input /path/to/fastq_pass
81
82 --output : Absolute path to directory where all the
83 pipeline outputs should be stored. Ex: --
84 output /path/to/output
85
86 Other options :
87
88 --metadata : Absolute path to metadata CSV file
89 containing five mandatory columns: sample,
90 fq1,fq2,strandedness,single_end. The fq1
91 and fq2 columns contain absolute paths to
92 the FASTQ files. This option can be used in
93 place of --input option. This is rare. Ex: --
94 metadata samplesheet.csv
95
96 --fq_suffix : The suffix of FASTQ files (Unpaired reads
97 or R1 reads or Long reads) if an input
98 directory is mentioned via --input option.
99 Default: _R1_001.fastq.gz
100
101 --fq2_suffix : The suffix of FASTQ files (Paired-end reads
102 or R2 reads) if an input directory is
103 mentioned via --input option. Default:
104 _R2_001.fastq.gz
105
106 --fq_filter_by_len : Remove FASTQ reads that are less than this
107 many bases. Default: 75
108
109 --fq_strandedness : The strandedness of the sequencing run.
110 This is mostly needed if your sequencing
111 run is RNA-SEQ. For most of the other runs,
112 it is probably safe to use unstranded for
113 the option. Default: unstranded
114
115 --fq_single_end : SINGLE-END information will be auto-
116 detected but this option forces PAIRED-END
117 FASTQ files to be treated as SINGLE-END so
118 only read 1 information is included in auto-
119 generated samplesheet. Default: false
120
121 --fq_filename_delim : Delimiter by which the file name is split
122 to obtain sample name. Default: _
123
124 --fq_filename_delim_idx : After splitting FASTQ file name by using
125 the --fq_filename_delim option, all
126 elements before this index (1-based) will
127 be joined to create final sample name.
128 Default: 1
129
130 --kraken2_db : Absolute path to kraken database. Default: /
131 hpc/db/kraken2/standard-210914
132
133 --kraken2_confidence : Confidence score threshold which must be
134 between 0 and 1. Default: 0.0
135
136 --kraken2_quick : Quick operation (use first hit or hits).
137 Default: false
138
139 --kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa-
140 report. Default: false
141
142 --kraken2_minimum_base_quality : Minimum base quality used in classification
143 which is only effective with FASTQ input.
144 Default: 0
145
146 --kraken2_report_zero_counts : Report counts for ALL taxa, even if counts
147 are zero. Default: false
148
149 --kraken2_report_minmizer_data : Report minimizer and distinct minimizer
150 count information in addition to normal
151 Kraken report. Default: false
152
153 --kraken2_use_names : Print scientific names instead of just
154 taxids. Default: true
155
156 --kraken2_extract_bug : Extract the reads or contigs beloging to
157 this bug. Default: Escherichia coli
158
159 --centrifuge_x : Absolute path to centrifuge database.
160 Default: /hpc/db/centrifuge/2022-04-12/ab
161
162 --centrifuge_save_unaligned : Save SINGLE-END reads that did not align.
163 For PAIRED-END reads, save read pairs that
164 did not align concordantly. Default: false
165
166 --centrifuge_save_aligned : Save SINGLE-END reads that aligned. For
167 PAIRED-END reads, save read pairs that
168 aligned concordantly. Default: false
169
170 --centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default:
171 false
172
173 --centrifuge_extract_bug : Extract this bug from centrifuge results.
174 Default: Escherichia coli
175
176 --centrifuge_ignore_quals : Treat all quality values as 30 on Phred
177 scale. Default: false
178
179 --spades_isolate : This flag is highly recommended for high-
180 coverage isolate and multi-cell data.
181 Defaut: false
182
183 --spades_sc : This flag is required for MDA (single-cell)
184 data. Default: false
185
186 --spades_meta : This flag is required for metagenomic data.
187 Default: true
188
189 --spades_bio : This flag is required for biosytheticSPAdes
190 mode. Default: false
191
192 --spades_corona : This flag is required for coronaSPAdes mode.
193 Default: false
194
195 --spades_rna : This flag is required for RNA-Seq data.
196 Default: false
197
198 --spades_plasmid : Runs plasmidSPAdes pipeline for plasmid
199 detection. Default: false
200
201 --spades_metaviral : Runs metaviralSPAdes pipeline for virus
202 detection. Default: false
203
204 --spades_metaplasmid : Runs metaplasmidSPAdes pipeline for plasmid
205 detection in metagenomics datasets. Default:
206 false
207
208 --spades_rnaviral : This flag enables virus assembly module
209 from RNA-Seq data. Default: false
210
211 --spades_iontorrent : This flag is required for IonTorrent data.
212 Default: false
213
214 --spades_only_assembler : Runs only the SPAdes assembler module (
215 without read error correction).Default:
216 false
217
218 --spades_careful : Tries to reduce the number of mismatches
219 and short indels in the assembly. Default:
220 false
221
222 --spades_cov_cutoff : Coverage cutoff value (a positive float
223 number). Default: false
224
225 --spades_k : List of k-mer sizes (must be odd and less
226 than 128). Default: false
227
228 --spades_hmm : Directory with custom hmms that replace the
229 default ones (very rare). Default: false
230
231 --serotypefinder_run : Run SerotypeFinder tool. Default: true
232
233 --serotypefinder_x : Generate extended output files. Default:
234 true
235
236 --serotypefinder_db : Path to SerotypeFinder databases. Default: /
237 hpc/db/serotypefinder/2.0.2
238
239 --serotypefinder_min_threshold : Minimum percent identity (in float)
240 required for calling a hit. Default: 0.85
241
242 --serotypefinder_min_cov : Minumum percent coverage (in float)
243 required for calling a hit. Default: 0.80
244
245 --seqsero2_run : Run SeqSero2 tool. Default: false
246
247 --seqsero2_t : '1' for interleaved paired-end reads, '2'
248 for separated paired-end reads, '3' for
249 single reads, '4' for genome assembly, '5'
250 for nanopore reads (fasta/fastq). Default:
251 4
252
253 --seqsero2_m : Which workflow to apply, 'a'(raw reads
254 allele micro-assembly), 'k'(raw reads and
255 genome assembly k-mer). Default: k
256
257 --seqsero2_c : SeqSero2 will only output serotype
258 prediction without the directory containing
259 log files. Default: false
260
261 --seqsero2_s : SeqSero2 will not output header in
262 SeqSero_result.tsv. Default: false
263
264 --mlst_run : Run MLST tool. Default: true
265
266 --mlst_minid : DNA %identity of full allelle to consider '
267 similar' [~]. Default: 95
268
269 --mlst_mincov : DNA %cov to report partial allele at all [?].
270 Default: 10
271
272 --mlst_minscore : Minumum score out of 100 to match a scheme.
273 Default: 50
274
275 --abricate_run : Run ABRicate tool. Default: true
276
277 --abricate_minid : Minimum DNA %identity. Defaut: 90
278
279 --abricate_mincov : Minimum DNA %coverage. Defaut: 80
280
281 --abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/
282 abricate/1.0.1/db
283
284 Help options :
285
286 --help : Display this message.
287 ```
288
289 ### **PRE ALPHA**
290
291 ---
292 This modular structure and flow is still in rapid development and may change
293 depending on assessment of various computational topics and other considerations