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author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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kkonganti@101 1 # CPIPES (CFSAN PIPELINES)
kkonganti@101 2
kkonganti@101 3 ## The modular pipeline repository at CFSAN, FDA
kkonganti@101 4
kkonganti@101 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@101 6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@101 7
kkonganti@101 8 ---
kkonganti@101 9
kkonganti@101 10 ### **centriflaken**
kkonganti@101 11
kkonganti@101 12 ---
kkonganti@101 13 Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli.
kkonganti@101 14
kkonganti@101 15 #### Workflow Usage
kkonganti@101 16
kkonganti@101 17 ```bash
kkonganti@101 18 module load cpipes/0.3.0
kkonganti@101 19
kkonganti@101 20 cpipes --pipeline centriflaken [options]
kkonganti@101 21 ```
kkonganti@101 22
kkonganti@101 23 Example: Run the default `centriflaken` pipeline with taxa of interest as *E. coli*.
kkonganti@101 24
kkonganti@101 25 ```bash
kkonganti@101 26 cd /hpc/scratch/$USER
kkonganti@101 27 mkdir nf-cpipes
kkonganti@101 28 cd nf-cpipes
kkonganti@101 29 cpipes --pipeline centriflaken --input /path/to/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov'
kkonganti@101 30 ```
kkonganti@101 31
kkonganti@101 32 Example: Run the `centriflaken` pipeline with taxa of interest as *Salmonella*. In this mode, `SerotypeFinder` tool will be replaced with `SeqSero2` tool.
kkonganti@101 33
kkonganti@101 34 ```bash
kkonganti@101 35 cd /hpc/scratch/$USER
kkonganti@101 36 mkdir nf-cpipes
kkonganti@101 37 cd nf-cpipes
kkonganti@101 38 cpipes --pipeline centriflaken --centrifuge_extract_bug 'Salmonella' --input /path/to/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov'
kkonganti@101 39 ```
kkonganti@101 40
kkonganti@101 41 #### `centriflaken` Help
kkonganti@101 42
kkonganti@101 43 ```text
kkonganti@101 44 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken --help
kkonganti@101 45 N E X T F L O W ~ version 21.12.1-edge
kkonganti@101 46 Launching `/nfs/software/apps/cpipes/0.2.1/cpipes` [drunk_ptolemy] - revision: 72db279311
kkonganti@101 47 ================================================================================
kkonganti@101 48 (o)
kkonganti@101 49 ___ _ __ _ _ __ ___ ___
kkonganti@101 50 / __|| '_ \ | || '_ \ / _ \/ __|
kkonganti@101 51 | (__ | |_) || || |_) || __/\__ \
kkonganti@101 52 \___|| .__/ |_|| .__/ \___||___/
kkonganti@101 53 | | | |
kkonganti@101 54 |_| |_|
kkonganti@101 55 --------------------------------------------------------------------------------
kkonganti@101 56 A collection of modular pipelines at CFSAN, FDA.
kkonganti@101 57 --------------------------------------------------------------------------------
kkonganti@101 58 Name : CPIPES
kkonganti@101 59 Author : Kranti.Konganti@fda.hhs.gov
kkonganti@101 60 Version : 0.2.1
kkonganti@101 61 Center : CFSAN, FDA.
kkonganti@101 62 ================================================================================
kkonganti@101 63
kkonganti@101 64 Workflow : centriflaken
kkonganti@101 65
kkonganti@101 66 Author : Kranti.Konganti@fda.hhs.gov
kkonganti@101 67
kkonganti@101 68 Version : 0.2.0
kkonganti@101 69
kkonganti@101 70
kkonganti@101 71 Usage : cpipes --pipeline centriflaken [options]
kkonganti@101 72
kkonganti@101 73
kkonganti@101 74 Required :
kkonganti@101 75
kkonganti@101 76 --input : Absolute path to directory containing FASTQ
kkonganti@101 77 files. The directory should contain only
kkonganti@101 78 FASTQ files as all the files within the
kkonganti@101 79 mentioned directory will be read. Ex: --
kkonganti@101 80 input /path/to/fastq_pass
kkonganti@101 81
kkonganti@101 82 --output : Absolute path to directory where all the
kkonganti@101 83 pipeline outputs should be stored. Ex: --
kkonganti@101 84 output /path/to/output
kkonganti@101 85
kkonganti@101 86 Other options :
kkonganti@101 87
kkonganti@101 88 --metadata : Absolute path to metadata CSV file
kkonganti@101 89 containing five mandatory columns: sample,
kkonganti@101 90 fq1,fq2,strandedness,single_end. The fq1
kkonganti@101 91 and fq2 columns contain absolute paths to
kkonganti@101 92 the FASTQ files. This option can be used in
kkonganti@101 93 place of --input option. This is rare. Ex: --
kkonganti@101 94 metadata samplesheet.csv
kkonganti@101 95
kkonganti@101 96 --fq_suffix : The suffix of FASTQ files (Unpaired reads
kkonganti@101 97 or R1 reads or Long reads) if an input
kkonganti@101 98 directory is mentioned via --input option.
kkonganti@101 99 Default: .fastq.gz
kkonganti@101 100
kkonganti@101 101 --fq2_suffix : The suffix of FASTQ files (Paired-end reads
kkonganti@101 102 or R2 reads) if an input directory is
kkonganti@101 103 mentioned via --input option. Default:
kkonganti@101 104 false
kkonganti@101 105
kkonganti@101 106 --fq_filter_by_len : Remove FASTQ reads that are less than this
kkonganti@101 107 many bases. Default: 4000
kkonganti@101 108
kkonganti@101 109 --fq_strandedness : The strandedness of the sequencing run.
kkonganti@101 110 This is mostly needed if your sequencing
kkonganti@101 111 run is RNA-SEQ. For most of the other runs,
kkonganti@101 112 it is probably safe to use unstranded for
kkonganti@101 113 the option. Default: unstranded
kkonganti@101 114
kkonganti@101 115 --fq_single_end : SINGLE-END information will be auto-
kkonganti@101 116 detected but this option forces PAIRED-END
kkonganti@101 117 FASTQ files to be treated as SINGLE-END so
kkonganti@101 118 only read 1 information is included in auto-
kkonganti@101 119 generated samplesheet. Default: false
kkonganti@101 120
kkonganti@101 121 --fq_filename_delim : Delimiter by which the file name is split
kkonganti@101 122 to obtain sample name. Default: _
kkonganti@101 123
kkonganti@101 124 --fq_filename_delim_idx : After splitting FASTQ file name by using
kkonganti@101 125 the --fq_filename_delim option, all
kkonganti@101 126 elements before this index (1-based) will
kkonganti@101 127 be joined to create final sample name.
kkonganti@101 128 Default: 1
kkonganti@101 129
kkonganti@101 130 --kraken2_db : Absolute path to kraken database. Default: /
kkonganti@101 131 hpc/db/kraken2/standard-210914
kkonganti@101 132
kkonganti@101 133 --kraken2_confidence : Confidence score threshold which must be
kkonganti@101 134 between 0 and 1. Default: 0.0
kkonganti@101 135
kkonganti@101 136 --kraken2_quick : Quick operation (use first hit or hits).
kkonganti@101 137 Default: false
kkonganti@101 138
kkonganti@101 139 --kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa-
kkonganti@101 140 report. Default: false
kkonganti@101 141
kkonganti@101 142 --kraken2_minimum_base_quality : Minimum base quality used in classification
kkonganti@101 143 which is only effective with FASTQ input.
kkonganti@101 144 Default: 0
kkonganti@101 145
kkonganti@101 146 --kraken2_report_zero_counts : Report counts for ALL taxa, even if counts
kkonganti@101 147 are zero. Default: false
kkonganti@101 148
kkonganti@101 149 --kraken2_report_minmizer_data : Report minimizer and distinct minimizer
kkonganti@101 150 count information in addition to normal
kkonganti@101 151 Kraken report. Default: false
kkonganti@101 152
kkonganti@101 153 --kraken2_use_names : Print scientific names instead of just
kkonganti@101 154 taxids. Default: true
kkonganti@101 155
kkonganti@101 156 --kraken2_extract_bug : Extract the reads or contigs beloging to
kkonganti@101 157 this bug. Default: Escherichia coli
kkonganti@101 158
kkonganti@101 159 --centrifuge_x : Absolute path to centrifuge database.
kkonganti@101 160 Default: /hpc/db/centrifuge/2022-04-12/ab
kkonganti@101 161
kkonganti@101 162 --centrifuge_save_unaligned : Save SINGLE-END reads that did not align.
kkonganti@101 163 For PAIRED-END reads, save read pairs that
kkonganti@101 164 did not align concordantly. Default: false
kkonganti@101 165
kkonganti@101 166 --centrifuge_save_aligned : Save SINGLE-END reads that aligned. For
kkonganti@101 167 PAIRED-END reads, save read pairs that
kkonganti@101 168 aligned concordantly. Default: false
kkonganti@101 169
kkonganti@101 170 --centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default:
kkonganti@101 171 false
kkonganti@101 172
kkonganti@101 173 --centrifuge_extract_bug : Extract this bug from centrifuge results.
kkonganti@101 174 Default: Escherichia coli
kkonganti@101 175
kkonganti@101 176 --centrifuge_ignore_quals : Treat all quality values as 30 on Phred
kkonganti@101 177 scale. Default: false
kkonganti@101 178
kkonganti@101 179 --flye_pacbio_raw : Input FASTQ reads are PacBio regular CLR
kkonganti@101 180 reads (<20% error) Defaut: false
kkonganti@101 181
kkonganti@101 182 --flye_pacbio_corr : Input FASTQ reads are PacBio reads that
kkonganti@101 183 were corrected with other methods (<3%
kkonganti@101 184 error). Default: false
kkonganti@101 185
kkonganti@101 186 --flye_pacbio_hifi : Input FASTQ reads are PacBio HiFi reads (<1%
kkonganti@101 187 error). Default: false
kkonganti@101 188
kkonganti@101 189 --flye_nano_raw : Input FASTQ reads are ONT regular reads,
kkonganti@101 190 pre-Guppy5 (<20% error). Default: true
kkonganti@101 191
kkonganti@101 192 --flye_nano_corr : Input FASTQ reads are ONT reads that were
kkonganti@101 193 corrected with other methods (<3% error).
kkonganti@101 194 Default: false
kkonganti@101 195
kkonganti@101 196 --flye_nano_hq : Input FASTQ reads are ONT high-quality
kkonganti@101 197 reads: Guppy5+ SUP or Q20 (<5% error).
kkonganti@101 198 Default: false
kkonganti@101 199
kkonganti@101 200 --flye_genome_size : Estimated genome size (for example, 5m or 2.
kkonganti@101 201 6g). Default: 5.5m
kkonganti@101 202
kkonganti@101 203 --flye_polish_iter : Number of genome polishing iterations.
kkonganti@101 204 Default: false
kkonganti@101 205
kkonganti@101 206 --flye_meta : Do a metagenome assembly (unenven coverage
kkonganti@101 207 mode). Default: true
kkonganti@101 208
kkonganti@101 209 --flye_min_overlap : Minimum overlap between reads. Default:
kkonganti@101 210 false
kkonganti@101 211
kkonganti@101 212 --flye_scaffold : Enable scaffolding using assembly graph.
kkonganti@101 213 Default: false
kkonganti@101 214
kkonganti@101 215 --serotypefinder_run : Run SerotypeFinder tool. Default: true
kkonganti@101 216
kkonganti@101 217 --serotypefinder_x : Generate extended output files. Default:
kkonganti@101 218 true
kkonganti@101 219
kkonganti@101 220 --serotypefinder_db : Path to SerotypeFinder databases. Default: /
kkonganti@101 221 hpc/db/serotypefinder/2.0.2
kkonganti@101 222
kkonganti@101 223 --serotypefinder_min_threshold : Minimum percent identity (in float)
kkonganti@101 224 required for calling a hit. Default: 0.85
kkonganti@101 225
kkonganti@101 226 --serotypefinder_min_cov : Minumum percent coverage (in float)
kkonganti@101 227 required for calling a hit. Default: 0.80
kkonganti@101 228
kkonganti@101 229 --seqsero2_run : Run SeqSero2 tool. Default: false
kkonganti@101 230
kkonganti@101 231 --seqsero2_t : '1' for interleaved paired-end reads, '2'
kkonganti@101 232 for separated paired-end reads, '3' for
kkonganti@101 233 single reads, '4' for genome assembly, '5'
kkonganti@101 234 for nanopore reads (fasta/fastq). Default:
kkonganti@101 235 4
kkonganti@101 236
kkonganti@101 237 --seqsero2_m : Which workflow to apply, 'a'(raw reads
kkonganti@101 238 allele micro-assembly), 'k'(raw reads and
kkonganti@101 239 genome assembly k-mer). Default: k
kkonganti@101 240
kkonganti@101 241 --seqsero2_c : SeqSero2 will only output serotype
kkonganti@101 242 prediction without the directory containing
kkonganti@101 243 log files. Default: false
kkonganti@101 244
kkonganti@101 245 --seqsero2_s : SeqSero2 will not output header in
kkonganti@101 246 SeqSero_result.tsv. Default: false
kkonganti@101 247
kkonganti@101 248 --mlst_run : Run MLST tool. Default: true
kkonganti@101 249
kkonganti@101 250 --mlst_minid : DNA %identity of full allelle to consider '
kkonganti@101 251 similar' [~]. Default: 95
kkonganti@101 252
kkonganti@101 253 --mlst_mincov : DNA %cov to report partial allele at all [?].
kkonganti@101 254 Default: 10
kkonganti@101 255
kkonganti@101 256 --mlst_minscore : Minumum score out of 100 to match a scheme.
kkonganti@101 257 Default: 50
kkonganti@101 258
kkonganti@101 259 --abricate_run : Run ABRicate tool. Default: true
kkonganti@101 260
kkonganti@101 261 --abricate_minid : Minimum DNA %identity. Defaut: 90
kkonganti@101 262
kkonganti@101 263 --abricate_mincov : Minimum DNA %coverage. Defaut: 80
kkonganti@101 264
kkonganti@101 265 --abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/
kkonganti@101 266 abricate/1.0.1/db
kkonganti@101 267
kkonganti@101 268 Help options :
kkonganti@101 269
kkonganti@101 270 --help : Display this message.
kkonganti@101 271 ```
kkonganti@101 272
kkonganti@101 273 ### **BETA**
kkonganti@101 274
kkonganti@101 275 ---
kkonganti@101 276 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.