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author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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kkonganti@0 1 # CPIPES (CFSAN PIPELINES)
kkonganti@0 2
kkonganti@0 3 ## The modular pipeline repository at CFSAN, FDA
kkonganti@0 4
kkonganti@0 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@0 6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@0 7
kkonganti@0 8 ---
kkonganti@0 9
kkonganti@0 10 ### **centriflaken_hy**
kkonganti@0 11
kkonganti@0 12 ---
kkonganti@0 13 `centriflaken_hy` is a variant of the original `centriflaken` pipeline but for Illumina short reads either single-end or paired-end.
kkonganti@0 14
kkonganti@0 15 #### Workflow Usage
kkonganti@0 16
kkonganti@0 17 ```bash
kkonganti@0 18 module load cpipes/0.4.0
kkonganti@0 19
kkonganti@0 20 cpipes --pipeline centriflaken_hy [options]
kkonganti@0 21 ```
kkonganti@0 22
kkonganti@0 23 Example: Run the default `centriflaken_hy` pipeline with taxa of interest as *E. coli*.
kkonganti@0 24
kkonganti@0 25 ```bash
kkonganti@0 26 cd /hpc/scratch/$USER
kkonganti@0 27 mkdir nf-cpipes
kkonganti@0 28 cd nf-cpipes
kkonganti@0 29 cpipes --pipeline centriflaken_hy --input /path/to/illumina/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov'
kkonganti@0 30 ```
kkonganti@0 31
kkonganti@0 32 Example: Run the `centriflaken_hy` pipeline with taxa of interest as *Salmonella*. In this mode, `SerotypeFinder` tool will be replaced with `SeqSero2` tool.
kkonganti@0 33
kkonganti@0 34 ```bash
kkonganti@0 35 cd /hpc/scratch/$USER
kkonganti@0 36 mkdir nf-cpipes
kkonganti@0 37 cd nf-cpipes
kkonganti@0 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@0 39 ```
kkonganti@0 40
kkonganti@0 41 #### `centriflaken_hy` Help
kkonganti@0 42
kkonganti@0 43 ```text
kkonganti@0 44 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help
kkonganti@0 45 N E X T F L O W ~ version 21.12.1-edge
kkonganti@0 46 Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [soggy_curie] - revision: 72db279311
kkonganti@0 47 ================================================================================
kkonganti@0 48 (o)
kkonganti@0 49 ___ _ __ _ _ __ ___ ___
kkonganti@0 50 / __|| '_ \ | || '_ \ / _ \/ __|
kkonganti@0 51 | (__ | |_) || || |_) || __/\__ \
kkonganti@0 52 \___|| .__/ |_|| .__/ \___||___/
kkonganti@0 53 | | | |
kkonganti@0 54 |_| |_|
kkonganti@0 55 --------------------------------------------------------------------------------
kkonganti@0 56 A collection of modular pipelines at CFSAN, FDA.
kkonganti@0 57 --------------------------------------------------------------------------------
kkonganti@0 58 Name : CPIPES
kkonganti@0 59 Author : Kranti.Konganti@fda.hhs.gov
kkonganti@0 60 Version : 0.4.0
kkonganti@0 61 Center : CFSAN, FDA.
kkonganti@0 62 ================================================================================
kkonganti@0 63
kkonganti@0 64 Workflow : centriflaken_hy
kkonganti@0 65
kkonganti@0 66 Author : Kranti.Konganti@fda.hhs.gov
kkonganti@0 67
kkonganti@0 68 Version : 0.4.0
kkonganti@0 69
kkonganti@0 70
kkonganti@0 71 Usage : cpipes --pipeline centriflaken_hy [options]
kkonganti@0 72
kkonganti@0 73
kkonganti@0 74 Required :
kkonganti@0 75
kkonganti@0 76 --input : Absolute path to directory containing FASTQ
kkonganti@0 77 files. The directory should contain only
kkonganti@0 78 FASTQ files as all the files within the
kkonganti@0 79 mentioned directory will be read. Ex: --
kkonganti@0 80 input /path/to/fastq_pass
kkonganti@0 81
kkonganti@0 82 --output : Absolute path to directory where all the
kkonganti@0 83 pipeline outputs should be stored. Ex: --
kkonganti@0 84 output /path/to/output
kkonganti@0 85
kkonganti@0 86 Other options :
kkonganti@0 87
kkonganti@0 88 --metadata : Absolute path to metadata CSV file
kkonganti@0 89 containing five mandatory columns: sample,
kkonganti@0 90 fq1,fq2,strandedness,single_end. The fq1
kkonganti@0 91 and fq2 columns contain absolute paths to
kkonganti@0 92 the FASTQ files. This option can be used in
kkonganti@0 93 place of --input option. This is rare. Ex: --
kkonganti@0 94 metadata samplesheet.csv
kkonganti@0 95
kkonganti@0 96 --fq_suffix : The suffix of FASTQ files (Unpaired reads
kkonganti@0 97 or R1 reads or Long reads) if an input
kkonganti@0 98 directory is mentioned via --input option.
kkonganti@0 99 Default: _R1_001.fastq.gz
kkonganti@0 100
kkonganti@0 101 --fq2_suffix : The suffix of FASTQ files (Paired-end reads
kkonganti@0 102 or R2 reads) if an input directory is
kkonganti@0 103 mentioned via --input option. Default:
kkonganti@0 104 _R2_001.fastq.gz
kkonganti@0 105
kkonganti@0 106 --fq_filter_by_len : Remove FASTQ reads that are less than this
kkonganti@0 107 many bases. Default: 75
kkonganti@0 108
kkonganti@0 109 --fq_strandedness : The strandedness of the sequencing run.
kkonganti@0 110 This is mostly needed if your sequencing
kkonganti@0 111 run is RNA-SEQ. For most of the other runs,
kkonganti@0 112 it is probably safe to use unstranded for
kkonganti@0 113 the option. Default: unstranded
kkonganti@0 114
kkonganti@0 115 --fq_single_end : SINGLE-END information will be auto-
kkonganti@0 116 detected but this option forces PAIRED-END
kkonganti@0 117 FASTQ files to be treated as SINGLE-END so
kkonganti@0 118 only read 1 information is included in auto-
kkonganti@0 119 generated samplesheet. Default: false
kkonganti@0 120
kkonganti@0 121 --fq_filename_delim : Delimiter by which the file name is split
kkonganti@0 122 to obtain sample name. Default: _
kkonganti@0 123
kkonganti@0 124 --fq_filename_delim_idx : After splitting FASTQ file name by using
kkonganti@0 125 the --fq_filename_delim option, all
kkonganti@0 126 elements before this index (1-based) will
kkonganti@0 127 be joined to create final sample name.
kkonganti@0 128 Default: 1
kkonganti@0 129
kkonganti@0 130 --seqkit_rmdup_run : Remove duplicate sequences using seqkit
kkonganti@0 131 rmdup. Default: false
kkonganti@0 132
kkonganti@0 133 --seqkit_rmdup_n : Match and remove duplicate sequences by
kkonganti@0 134 full name instead of just ID. Defaut: false
kkonganti@0 135
kkonganti@0 136 --seqkit_rmdup_s : Match and remove duplicate sequences by
kkonganti@0 137 sequence content. Defaut: true
kkonganti@0 138
kkonganti@0 139 --seqkit_rmdup_d : Save the duplicated sequences to a file.
kkonganti@0 140 Defaut: false
kkonganti@0 141
kkonganti@0 142 --seqkit_rmdup_D : Save the number and list of duplicated
kkonganti@0 143 sequences to a file. Defaut: false
kkonganti@0 144
kkonganti@0 145 --seqkit_rmdup_i : Ignore case while using seqkit rmdup.
kkonganti@0 146 Defaut: false
kkonganti@0 147
kkonganti@0 148 --seqkit_rmdup_P : Only consider positive strand (i.e. 5')
kkonganti@0 149 when comparing by sequence content. Defaut:
kkonganti@0 150 false
kkonganti@0 151
kkonganti@0 152 --kraken2_db : Absolute path to kraken database. Default: /
kkonganti@0 153 hpc/db/kraken2/standard-210914
kkonganti@0 154
kkonganti@0 155 --kraken2_confidence : Confidence score threshold which must be
kkonganti@0 156 between 0 and 1. Default: 0.0
kkonganti@0 157
kkonganti@0 158 --kraken2_quick : Quick operation (use first hit or hits).
kkonganti@0 159 Default: false
kkonganti@0 160
kkonganti@0 161 --kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa-
kkonganti@0 162 report. Default: false
kkonganti@0 163
kkonganti@0 164 --kraken2_minimum_base_quality : Minimum base quality used in classification
kkonganti@0 165 which is only effective with FASTQ input.
kkonganti@0 166 Default: 0
kkonganti@0 167
kkonganti@0 168 --kraken2_report_zero_counts : Report counts for ALL taxa, even if counts
kkonganti@0 169 are zero. Default: false
kkonganti@0 170
kkonganti@0 171 --kraken2_report_minmizer_data : Report minimizer and distinct minimizer
kkonganti@0 172 count information in addition to normal
kkonganti@0 173 Kraken report. Default: false
kkonganti@0 174
kkonganti@0 175 --kraken2_use_names : Print scientific names instead of just
kkonganti@0 176 taxids. Default: true
kkonganti@0 177
kkonganti@0 178 --kraken2_extract_bug : Extract the reads or contigs beloging to
kkonganti@0 179 this bug. Default: Escherichia coli
kkonganti@0 180
kkonganti@0 181 --centrifuge_x : Absolute path to centrifuge database.
kkonganti@0 182 Default: /hpc/db/centrifuge/2022-04-12/ab
kkonganti@0 183
kkonganti@0 184 --centrifuge_save_unaligned : Save SINGLE-END reads that did not align.
kkonganti@0 185 For PAIRED-END reads, save read pairs that
kkonganti@0 186 did not align concordantly. Default: false
kkonganti@0 187
kkonganti@0 188 --centrifuge_save_aligned : Save SINGLE-END reads that aligned. For
kkonganti@0 189 PAIRED-END reads, save read pairs that
kkonganti@0 190 aligned concordantly. Default: false
kkonganti@0 191
kkonganti@0 192 --centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default:
kkonganti@0 193 false
kkonganti@0 194
kkonganti@0 195 --centrifuge_extract_bug : Extract this bug from centrifuge results.
kkonganti@0 196 Default: Escherichia coli
kkonganti@0 197
kkonganti@0 198 --centrifuge_ignore_quals : Treat all quality values as 30 on Phred
kkonganti@0 199 scale. Default: false
kkonganti@0 200
kkonganti@0 201 --megahit_run : Run MEGAHIT assembler. Default: true
kkonganti@0 202
kkonganti@0 203 --megahit_min_count : <int>. Minimum multiplicity for filtering (
kkonganti@0 204 k_min+1)-mers. Defaut: false
kkonganti@0 205
kkonganti@0 206 --megahit_k_list : Comma-separated list of kmer size. All
kkonganti@0 207 values must be odd, in the range 15-255,
kkonganti@0 208 increment should be <= 28. Ex: '21,29,39,59,
kkonganti@0 209 79,99,119,141'. Default: false
kkonganti@0 210
kkonganti@0 211 --megahit_no_mercy : Do not add mercy k-mers. Default: false
kkonganti@0 212
kkonganti@0 213 --megahit_bubble_level : <int>. Intensity of bubble merging (0-2), 0
kkonganti@0 214 to disable. Default: false
kkonganti@0 215
kkonganti@0 216 --megahit_merge_level : <l,s>. Merge complex bubbles of length <= l*
kkonganti@0 217 kmer_size and similarity >= s. Default:
kkonganti@0 218 false
kkonganti@0 219
kkonganti@0 220 --megahit_prune_level : <int>. Strength of low depth pruning (0-3).
kkonganti@0 221 Default: false
kkonganti@0 222
kkonganti@0 223 --megahit_prune_depth : <int>. Remove unitigs with avg k-mer depth
kkonganti@0 224 less than this value. Default: false
kkonganti@0 225
kkonganti@0 226 --megahit_low_local_ratio : <float>. Ratio threshold to define low
kkonganti@0 227 local coverage contigs. Default: false
kkonganti@0 228
kkonganti@0 229 --megahit_max_tip_len : <int>. remove tips less than this value [<
kkonganti@0 230 int> * k]. Default: false
kkonganti@0 231
kkonganti@0 232 --megahit_no_local : Disable local assembly. Default: false
kkonganti@0 233
kkonganti@0 234 --megahit_kmin_1pass : Use 1pass mode to build SdBG of k_min.
kkonganti@0 235 Default: false
kkonganti@0 236
kkonganti@0 237 --megahit_preset : <str>. Override a group of parameters.
kkonganti@0 238 Valid values are meta-sensitive which
kkonganti@0 239 enforces '--min-count 1 --k-list 21,29,39,
kkonganti@0 240 49,...,129,141', meta-large (large &
kkonganti@0 241 complex metagenomes, like soil) which
kkonganti@0 242 enforces '--k-min 27 --k-max 127 --k-step
kkonganti@0 243 10'. Default: meta-sensitive
kkonganti@0 244
kkonganti@0 245 --megahit_mem_flag : <int>. SdBG builder memory mode. 0: minimum;
kkonganti@0 246 1: moderate; 2: use all memory specified.
kkonganti@0 247 Default: 2
kkonganti@0 248
kkonganti@0 249 --megahit_min_contig_len : <int>. Minimum length of contigs to output.
kkonganti@0 250 Default: false
kkonganti@0 251
kkonganti@0 252 --spades_run : Run SPAdes assembler. Default: false
kkonganti@0 253
kkonganti@0 254 --spades_isolate : This flag is highly recommended for high-
kkonganti@0 255 coverage isolate and multi-cell data.
kkonganti@0 256 Defaut: false
kkonganti@0 257
kkonganti@0 258 --spades_sc : This flag is required for MDA (single-cell)
kkonganti@0 259 data. Default: false
kkonganti@0 260
kkonganti@0 261 --spades_meta : This flag is required for metagenomic data.
kkonganti@0 262 Default: true
kkonganti@0 263
kkonganti@0 264 --spades_bio : This flag is required for biosytheticSPAdes
kkonganti@0 265 mode. Default: false
kkonganti@0 266
kkonganti@0 267 --spades_corona : This flag is required for coronaSPAdes mode.
kkonganti@0 268 Default: false
kkonganti@0 269
kkonganti@0 270 --spades_rna : This flag is required for RNA-Seq data.
kkonganti@0 271 Default: false
kkonganti@0 272
kkonganti@0 273 --spades_plasmid : Runs plasmidSPAdes pipeline for plasmid
kkonganti@0 274 detection. Default: false
kkonganti@0 275
kkonganti@0 276 --spades_metaviral : Runs metaviralSPAdes pipeline for virus
kkonganti@0 277 detection. Default: false
kkonganti@0 278
kkonganti@0 279 --spades_metaplasmid : Runs metaplasmidSPAdes pipeline for plasmid
kkonganti@0 280 detection in metagenomics datasets. Default:
kkonganti@0 281 false
kkonganti@0 282
kkonganti@0 283 --spades_rnaviral : This flag enables virus assembly module
kkonganti@0 284 from RNA-Seq data. Default: false
kkonganti@0 285
kkonganti@0 286 --spades_iontorrent : This flag is required for IonTorrent data.
kkonganti@0 287 Default: false
kkonganti@0 288
kkonganti@0 289 --spades_only_assembler : Runs only the SPAdes assembler module (
kkonganti@0 290 without read error correction). Default:
kkonganti@0 291 false
kkonganti@0 292
kkonganti@0 293 --spades_careful : Tries to reduce the number of mismatches
kkonganti@0 294 and short indels in the assembly. Default:
kkonganti@0 295 false
kkonganti@0 296
kkonganti@0 297 --spades_cov_cutoff : Coverage cutoff value (a positive float
kkonganti@0 298 number). Default: false
kkonganti@0 299
kkonganti@0 300 --spades_k : List of k-mer sizes (must be odd and less
kkonganti@0 301 than 128). Default: false
kkonganti@0 302
kkonganti@0 303 --spades_hmm : Directory with custom hmms that replace the
kkonganti@0 304 default ones (very rare). Default: false
kkonganti@0 305
kkonganti@0 306 --serotypefinder_run : Run SerotypeFinder tool. Default: true
kkonganti@0 307
kkonganti@0 308 --serotypefinder_x : Generate extended output files. Default:
kkonganti@0 309 true
kkonganti@0 310
kkonganti@0 311 --serotypefinder_db : Path to SerotypeFinder databases. Default: /
kkonganti@0 312 hpc/db/serotypefinder/2.0.2
kkonganti@0 313
kkonganti@0 314 --serotypefinder_min_threshold : Minimum percent identity (in float)
kkonganti@0 315 required for calling a hit. Default: 0.85
kkonganti@0 316
kkonganti@0 317 --serotypefinder_min_cov : Minumum percent coverage (in float)
kkonganti@0 318 required for calling a hit. Default: 0.80
kkonganti@0 319
kkonganti@0 320 --seqsero2_run : Run SeqSero2 tool. Default: false
kkonganti@0 321
kkonganti@0 322 --seqsero2_t : '1' for interleaved paired-end reads, '2'
kkonganti@0 323 for separated paired-end reads, '3' for
kkonganti@0 324 single reads, '4' for genome assembly, '5'
kkonganti@0 325 for nanopore reads (fasta/fastq). Default:
kkonganti@0 326 4
kkonganti@0 327
kkonganti@0 328 --seqsero2_m : Which workflow to apply, 'a'(raw reads
kkonganti@0 329 allele micro-assembly), 'k'(raw reads and
kkonganti@0 330 genome assembly k-mer). Default: k
kkonganti@0 331
kkonganti@0 332 --seqsero2_c : SeqSero2 will only output serotype
kkonganti@0 333 prediction without the directory containing
kkonganti@0 334 log files. Default: false
kkonganti@0 335
kkonganti@0 336 --seqsero2_s : SeqSero2 will not output header in
kkonganti@0 337 SeqSero_result.tsv. Default: false
kkonganti@0 338
kkonganti@0 339 --mlst_run : Run MLST tool. Default: true
kkonganti@0 340
kkonganti@0 341 --mlst_minid : DNA %identity of full allelle to consider '
kkonganti@0 342 similar' [~]. Default: 95
kkonganti@0 343
kkonganti@0 344 --mlst_mincov : DNA %cov to report partial allele at all [?].
kkonganti@0 345 Default: 10
kkonganti@0 346
kkonganti@0 347 --mlst_minscore : Minumum score out of 100 to match a scheme.
kkonganti@0 348 Default: 50
kkonganti@0 349
kkonganti@0 350 --abricate_run : Run ABRicate tool. Default: true
kkonganti@0 351
kkonganti@0 352 --abricate_minid : Minimum DNA %identity. Defaut: 90
kkonganti@0 353
kkonganti@0 354 --abricate_mincov : Minimum DNA %coverage. Defaut: 80
kkonganti@0 355
kkonganti@0 356 --abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/
kkonganti@0 357 abricate/1.0.1/db
kkonganti@0 358
kkonganti@0 359 Help options :
kkonganti@0 360
kkonganti@0 361 --help : Display this message.
kkonganti@0 362 ```
kkonganti@0 363
kkonganti@0 364 ### **BETA**
kkonganti@0 365
kkonganti@0 366 ---
kkonganti@0 367 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.