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author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
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kkonganti@105 1 # CPIPES (CFSAN PIPELINES)
kkonganti@105 2
kkonganti@105 3 ## The modular pipeline repository at CFSAN, FDA
kkonganti@105 4
kkonganti@105 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@105 6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@105 7
kkonganti@105 8 ---
kkonganti@105 9
kkonganti@105 10 ### **centriflaken_hy**
kkonganti@105 11
kkonganti@105 12 ---
kkonganti@105 13 `centriflaken_hy` is a variant of the original `centriflaken` pipeline but for Illumina short reads either single-end or paired-end.
kkonganti@105 14
kkonganti@105 15 #### Workflow Usage
kkonganti@105 16
kkonganti@105 17 ```bash
kkonganti@105 18 module load cpipes/0.4.0
kkonganti@105 19
kkonganti@105 20 cpipes --pipeline centriflaken_hy [options]
kkonganti@105 21 ```
kkonganti@105 22
kkonganti@105 23 Example: Run the default `centriflaken_hy` pipeline with taxa of interest as *E. coli*.
kkonganti@105 24
kkonganti@105 25 ```bash
kkonganti@105 26 cd /hpc/scratch/$USER
kkonganti@105 27 mkdir nf-cpipes
kkonganti@105 28 cd nf-cpipes
kkonganti@105 29 cpipes --pipeline centriflaken_hy --input /path/to/illumina/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov'
kkonganti@105 30 ```
kkonganti@105 31
kkonganti@105 32 Example: Run the `centriflaken_hy` pipeline with taxa of interest as *Salmonella*. In this mode, `SerotypeFinder` tool will be replaced with `SeqSero2` tool.
kkonganti@105 33
kkonganti@105 34 ```bash
kkonganti@105 35 cd /hpc/scratch/$USER
kkonganti@105 36 mkdir nf-cpipes
kkonganti@105 37 cd nf-cpipes
kkonganti@105 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'
kkonganti@105 39 ```
kkonganti@105 40
kkonganti@105 41 #### `centriflaken_hy` Help
kkonganti@105 42
kkonganti@105 43 ```text
kkonganti@105 44 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help
kkonganti@105 45 N E X T F L O W ~ version 21.12.1-edge
kkonganti@105 46 Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [soggy_curie] - revision: 72db279311
kkonganti@105 47 ================================================================================
kkonganti@105 48 (o)
kkonganti@105 49 ___ _ __ _ _ __ ___ ___
kkonganti@105 50 / __|| '_ \ | || '_ \ / _ \/ __|
kkonganti@105 51 | (__ | |_) || || |_) || __/\__ \
kkonganti@105 52 \___|| .__/ |_|| .__/ \___||___/
kkonganti@105 53 | | | |
kkonganti@105 54 |_| |_|
kkonganti@105 55 --------------------------------------------------------------------------------
kkonganti@105 56 A collection of modular pipelines at CFSAN, FDA.
kkonganti@105 57 --------------------------------------------------------------------------------
kkonganti@105 58 Name : CPIPES
kkonganti@105 59 Author : Kranti.Konganti@fda.hhs.gov
kkonganti@105 60 Version : 0.4.0
kkonganti@105 61 Center : CFSAN, FDA.
kkonganti@105 62 ================================================================================
kkonganti@105 63
kkonganti@105 64 Workflow : centriflaken_hy
kkonganti@105 65
kkonganti@105 66 Author : Kranti.Konganti@fda.hhs.gov
kkonganti@105 67
kkonganti@105 68 Version : 0.4.0
kkonganti@105 69
kkonganti@105 70
kkonganti@105 71 Usage : cpipes --pipeline centriflaken_hy [options]
kkonganti@105 72
kkonganti@105 73
kkonganti@105 74 Required :
kkonganti@105 75
kkonganti@105 76 --input : Absolute path to directory containing FASTQ
kkonganti@105 77 files. The directory should contain only
kkonganti@105 78 FASTQ files as all the files within the
kkonganti@105 79 mentioned directory will be read. Ex: --
kkonganti@105 80 input /path/to/fastq_pass
kkonganti@105 81
kkonganti@105 82 --output : Absolute path to directory where all the
kkonganti@105 83 pipeline outputs should be stored. Ex: --
kkonganti@105 84 output /path/to/output
kkonganti@105 85
kkonganti@105 86 Other options :
kkonganti@105 87
kkonganti@105 88 --metadata : Absolute path to metadata CSV file
kkonganti@105 89 containing five mandatory columns: sample,
kkonganti@105 90 fq1,fq2,strandedness,single_end. The fq1
kkonganti@105 91 and fq2 columns contain absolute paths to
kkonganti@105 92 the FASTQ files. This option can be used in
kkonganti@105 93 place of --input option. This is rare. Ex: --
kkonganti@105 94 metadata samplesheet.csv
kkonganti@105 95
kkonganti@105 96 --fq_suffix : The suffix of FASTQ files (Unpaired reads
kkonganti@105 97 or R1 reads or Long reads) if an input
kkonganti@105 98 directory is mentioned via --input option.
kkonganti@105 99 Default: _R1_001.fastq.gz
kkonganti@105 100
kkonganti@105 101 --fq2_suffix : The suffix of FASTQ files (Paired-end reads
kkonganti@105 102 or R2 reads) if an input directory is
kkonganti@105 103 mentioned via --input option. Default:
kkonganti@105 104 _R2_001.fastq.gz
kkonganti@105 105
kkonganti@105 106 --fq_filter_by_len : Remove FASTQ reads that are less than this
kkonganti@105 107 many bases. Default: 75
kkonganti@105 108
kkonganti@105 109 --fq_strandedness : The strandedness of the sequencing run.
kkonganti@105 110 This is mostly needed if your sequencing
kkonganti@105 111 run is RNA-SEQ. For most of the other runs,
kkonganti@105 112 it is probably safe to use unstranded for
kkonganti@105 113 the option. Default: unstranded
kkonganti@105 114
kkonganti@105 115 --fq_single_end : SINGLE-END information will be auto-
kkonganti@105 116 detected but this option forces PAIRED-END
kkonganti@105 117 FASTQ files to be treated as SINGLE-END so
kkonganti@105 118 only read 1 information is included in auto-
kkonganti@105 119 generated samplesheet. Default: false
kkonganti@105 120
kkonganti@105 121 --fq_filename_delim : Delimiter by which the file name is split
kkonganti@105 122 to obtain sample name. Default: _
kkonganti@105 123
kkonganti@105 124 --fq_filename_delim_idx : After splitting FASTQ file name by using
kkonganti@105 125 the --fq_filename_delim option, all
kkonganti@105 126 elements before this index (1-based) will
kkonganti@105 127 be joined to create final sample name.
kkonganti@105 128 Default: 1
kkonganti@105 129
kkonganti@105 130 --seqkit_rmdup_run : Remove duplicate sequences using seqkit
kkonganti@105 131 rmdup. Default: false
kkonganti@105 132
kkonganti@105 133 --seqkit_rmdup_n : Match and remove duplicate sequences by
kkonganti@105 134 full name instead of just ID. Defaut: false
kkonganti@105 135
kkonganti@105 136 --seqkit_rmdup_s : Match and remove duplicate sequences by
kkonganti@105 137 sequence content. Defaut: true
kkonganti@105 138
kkonganti@105 139 --seqkit_rmdup_d : Save the duplicated sequences to a file.
kkonganti@105 140 Defaut: false
kkonganti@105 141
kkonganti@105 142 --seqkit_rmdup_D : Save the number and list of duplicated
kkonganti@105 143 sequences to a file. Defaut: false
kkonganti@105 144
kkonganti@105 145 --seqkit_rmdup_i : Ignore case while using seqkit rmdup.
kkonganti@105 146 Defaut: false
kkonganti@105 147
kkonganti@105 148 --seqkit_rmdup_P : Only consider positive strand (i.e. 5')
kkonganti@105 149 when comparing by sequence content. Defaut:
kkonganti@105 150 false
kkonganti@105 151
kkonganti@105 152 --kraken2_db : Absolute path to kraken database. Default: /
kkonganti@105 153 hpc/db/kraken2/standard-210914
kkonganti@105 154
kkonganti@105 155 --kraken2_confidence : Confidence score threshold which must be
kkonganti@105 156 between 0 and 1. Default: 0.0
kkonganti@105 157
kkonganti@105 158 --kraken2_quick : Quick operation (use first hit or hits).
kkonganti@105 159 Default: false
kkonganti@105 160
kkonganti@105 161 --kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa-
kkonganti@105 162 report. Default: false
kkonganti@105 163
kkonganti@105 164 --kraken2_minimum_base_quality : Minimum base quality used in classification
kkonganti@105 165 which is only effective with FASTQ input.
kkonganti@105 166 Default: 0
kkonganti@105 167
kkonganti@105 168 --kraken2_report_zero_counts : Report counts for ALL taxa, even if counts
kkonganti@105 169 are zero. Default: false
kkonganti@105 170
kkonganti@105 171 --kraken2_report_minmizer_data : Report minimizer and distinct minimizer
kkonganti@105 172 count information in addition to normal
kkonganti@105 173 Kraken report. Default: false
kkonganti@105 174
kkonganti@105 175 --kraken2_use_names : Print scientific names instead of just
kkonganti@105 176 taxids. Default: true
kkonganti@105 177
kkonganti@105 178 --kraken2_extract_bug : Extract the reads or contigs beloging to
kkonganti@105 179 this bug. Default: Escherichia coli
kkonganti@105 180
kkonganti@105 181 --centrifuge_x : Absolute path to centrifuge database.
kkonganti@105 182 Default: /hpc/db/centrifuge/2022-04-12/ab
kkonganti@105 183
kkonganti@105 184 --centrifuge_save_unaligned : Save SINGLE-END reads that did not align.
kkonganti@105 185 For PAIRED-END reads, save read pairs that
kkonganti@105 186 did not align concordantly. Default: false
kkonganti@105 187
kkonganti@105 188 --centrifuge_save_aligned : Save SINGLE-END reads that aligned. For
kkonganti@105 189 PAIRED-END reads, save read pairs that
kkonganti@105 190 aligned concordantly. Default: false
kkonganti@105 191
kkonganti@105 192 --centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default:
kkonganti@105 193 false
kkonganti@105 194
kkonganti@105 195 --centrifuge_extract_bug : Extract this bug from centrifuge results.
kkonganti@105 196 Default: Escherichia coli
kkonganti@105 197
kkonganti@105 198 --centrifuge_ignore_quals : Treat all quality values as 30 on Phred
kkonganti@105 199 scale. Default: false
kkonganti@105 200
kkonganti@105 201 --megahit_run : Run MEGAHIT assembler. Default: true
kkonganti@105 202
kkonganti@105 203 --megahit_min_count : <int>. Minimum multiplicity for filtering (
kkonganti@105 204 k_min+1)-mers. Defaut: false
kkonganti@105 205
kkonganti@105 206 --megahit_k_list : Comma-separated list of kmer size. All
kkonganti@105 207 values must be odd, in the range 15-255,
kkonganti@105 208 increment should be <= 28. Ex: '21,29,39,59,
kkonganti@105 209 79,99,119,141'. Default: false
kkonganti@105 210
kkonganti@105 211 --megahit_no_mercy : Do not add mercy k-mers. Default: false
kkonganti@105 212
kkonganti@105 213 --megahit_bubble_level : <int>. Intensity of bubble merging (0-2), 0
kkonganti@105 214 to disable. Default: false
kkonganti@105 215
kkonganti@105 216 --megahit_merge_level : <l,s>. Merge complex bubbles of length <= l*
kkonganti@105 217 kmer_size and similarity >= s. Default:
kkonganti@105 218 false
kkonganti@105 219
kkonganti@105 220 --megahit_prune_level : <int>. Strength of low depth pruning (0-3).
kkonganti@105 221 Default: false
kkonganti@105 222
kkonganti@105 223 --megahit_prune_depth : <int>. Remove unitigs with avg k-mer depth
kkonganti@105 224 less than this value. Default: false
kkonganti@105 225
kkonganti@105 226 --megahit_low_local_ratio : <float>. Ratio threshold to define low
kkonganti@105 227 local coverage contigs. Default: false
kkonganti@105 228
kkonganti@105 229 --megahit_max_tip_len : <int>. remove tips less than this value [<
kkonganti@105 230 int> * k]. Default: false
kkonganti@105 231
kkonganti@105 232 --megahit_no_local : Disable local assembly. Default: false
kkonganti@105 233
kkonganti@105 234 --megahit_kmin_1pass : Use 1pass mode to build SdBG of k_min.
kkonganti@105 235 Default: false
kkonganti@105 236
kkonganti@105 237 --megahit_preset : <str>. Override a group of parameters.
kkonganti@105 238 Valid values are meta-sensitive which
kkonganti@105 239 enforces '--min-count 1 --k-list 21,29,39,
kkonganti@105 240 49,...,129,141', meta-large (large &
kkonganti@105 241 complex metagenomes, like soil) which
kkonganti@105 242 enforces '--k-min 27 --k-max 127 --k-step
kkonganti@105 243 10'. Default: meta-sensitive
kkonganti@105 244
kkonganti@105 245 --megahit_mem_flag : <int>. SdBG builder memory mode. 0: minimum;
kkonganti@105 246 1: moderate; 2: use all memory specified.
kkonganti@105 247 Default: 2
kkonganti@105 248
kkonganti@105 249 --megahit_min_contig_len : <int>. Minimum length of contigs to output.
kkonganti@105 250 Default: false
kkonganti@105 251
kkonganti@105 252 --spades_run : Run SPAdes assembler. Default: false
kkonganti@105 253
kkonganti@105 254 --spades_isolate : This flag is highly recommended for high-
kkonganti@105 255 coverage isolate and multi-cell data.
kkonganti@105 256 Defaut: false
kkonganti@105 257
kkonganti@105 258 --spades_sc : This flag is required for MDA (single-cell)
kkonganti@105 259 data. Default: false
kkonganti@105 260
kkonganti@105 261 --spades_meta : This flag is required for metagenomic data.
kkonganti@105 262 Default: true
kkonganti@105 263
kkonganti@105 264 --spades_bio : This flag is required for biosytheticSPAdes
kkonganti@105 265 mode. Default: false
kkonganti@105 266
kkonganti@105 267 --spades_corona : This flag is required for coronaSPAdes mode.
kkonganti@105 268 Default: false
kkonganti@105 269
kkonganti@105 270 --spades_rna : This flag is required for RNA-Seq data.
kkonganti@105 271 Default: false
kkonganti@105 272
kkonganti@105 273 --spades_plasmid : Runs plasmidSPAdes pipeline for plasmid
kkonganti@105 274 detection. Default: false
kkonganti@105 275
kkonganti@105 276 --spades_metaviral : Runs metaviralSPAdes pipeline for virus
kkonganti@105 277 detection. Default: false
kkonganti@105 278
kkonganti@105 279 --spades_metaplasmid : Runs metaplasmidSPAdes pipeline for plasmid
kkonganti@105 280 detection in metagenomics datasets. Default:
kkonganti@105 281 false
kkonganti@105 282
kkonganti@105 283 --spades_rnaviral : This flag enables virus assembly module
kkonganti@105 284 from RNA-Seq data. Default: false
kkonganti@105 285
kkonganti@105 286 --spades_iontorrent : This flag is required for IonTorrent data.
kkonganti@105 287 Default: false
kkonganti@105 288
kkonganti@105 289 --spades_only_assembler : Runs only the SPAdes assembler module (
kkonganti@105 290 without read error correction). Default:
kkonganti@105 291 false
kkonganti@105 292
kkonganti@105 293 --spades_careful : Tries to reduce the number of mismatches
kkonganti@105 294 and short indels in the assembly. Default:
kkonganti@105 295 false
kkonganti@105 296
kkonganti@105 297 --spades_cov_cutoff : Coverage cutoff value (a positive float
kkonganti@105 298 number). Default: false
kkonganti@105 299
kkonganti@105 300 --spades_k : List of k-mer sizes (must be odd and less
kkonganti@105 301 than 128). Default: false
kkonganti@105 302
kkonganti@105 303 --spades_hmm : Directory with custom hmms that replace the
kkonganti@105 304 default ones (very rare). Default: false
kkonganti@105 305
kkonganti@105 306 --serotypefinder_run : Run SerotypeFinder tool. Default: true
kkonganti@105 307
kkonganti@105 308 --serotypefinder_x : Generate extended output files. Default:
kkonganti@105 309 true
kkonganti@105 310
kkonganti@105 311 --serotypefinder_db : Path to SerotypeFinder databases. Default: /
kkonganti@105 312 hpc/db/serotypefinder/2.0.2
kkonganti@105 313
kkonganti@105 314 --serotypefinder_min_threshold : Minimum percent identity (in float)
kkonganti@105 315 required for calling a hit. Default: 0.85
kkonganti@105 316
kkonganti@105 317 --serotypefinder_min_cov : Minumum percent coverage (in float)
kkonganti@105 318 required for calling a hit. Default: 0.80
kkonganti@105 319
kkonganti@105 320 --seqsero2_run : Run SeqSero2 tool. Default: false
kkonganti@105 321
kkonganti@105 322 --seqsero2_t : '1' for interleaved paired-end reads, '2'
kkonganti@105 323 for separated paired-end reads, '3' for
kkonganti@105 324 single reads, '4' for genome assembly, '5'
kkonganti@105 325 for nanopore reads (fasta/fastq). Default:
kkonganti@105 326 4
kkonganti@105 327
kkonganti@105 328 --seqsero2_m : Which workflow to apply, 'a'(raw reads
kkonganti@105 329 allele micro-assembly), 'k'(raw reads and
kkonganti@105 330 genome assembly k-mer). Default: k
kkonganti@105 331
kkonganti@105 332 --seqsero2_c : SeqSero2 will only output serotype
kkonganti@105 333 prediction without the directory containing
kkonganti@105 334 log files. Default: false
kkonganti@105 335
kkonganti@105 336 --seqsero2_s : SeqSero2 will not output header in
kkonganti@105 337 SeqSero_result.tsv. Default: false
kkonganti@105 338
kkonganti@105 339 --mlst_run : Run MLST tool. Default: true
kkonganti@105 340
kkonganti@105 341 --mlst_minid : DNA %identity of full allelle to consider '
kkonganti@105 342 similar' [~]. Default: 95
kkonganti@105 343
kkonganti@105 344 --mlst_mincov : DNA %cov to report partial allele at all [?].
kkonganti@105 345 Default: 10
kkonganti@105 346
kkonganti@105 347 --mlst_minscore : Minumum score out of 100 to match a scheme.
kkonganti@105 348 Default: 50
kkonganti@105 349
kkonganti@105 350 --abricate_run : Run ABRicate tool. Default: true
kkonganti@105 351
kkonganti@105 352 --abricate_minid : Minimum DNA %identity. Defaut: 90
kkonganti@105 353
kkonganti@105 354 --abricate_mincov : Minimum DNA %coverage. Defaut: 80
kkonganti@105 355
kkonganti@105 356 --abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/
kkonganti@105 357 abricate/1.0.1/db
kkonganti@105 358
kkonganti@105 359 Help options :
kkonganti@105 360
kkonganti@105 361 --help : Display this message.
kkonganti@105 362 ```
kkonganti@105 363
kkonganti@105 364 ### **BETA**
kkonganti@105 365
kkonganti@105 366 ---
kkonganti@105 367 The development of the modular structure and flow is an ongoing effort and may change depending on assessment of various computational topics and other considerations.