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author kkonganti
date Mon, 27 Jun 2022 16:00:59 -0400
parents 77494b0fa3c7
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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/0.2.0
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 `/nfs/software/apps/cpipes/0.2.1/cpipes` [wise_noyce] - 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 : 0.2.1
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 : 0.2.0
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 --kraken2_db : Absolute path to kraken database. Default: /
kkonganti@0 131 hpc/db/kraken2/standard-210914
kkonganti@0 132
kkonganti@0 133 --kraken2_confidence : Confidence score threshold which must be
kkonganti@0 134 between 0 and 1. Default: 0.0
kkonganti@0 135
kkonganti@0 136 --kraken2_quick : Quick operation (use first hit or hits).
kkonganti@0 137 Default: false
kkonganti@0 138
kkonganti@0 139 --kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa-
kkonganti@0 140 report. Default: false
kkonganti@0 141
kkonganti@0 142 --kraken2_minimum_base_quality : Minimum base quality used in classification
kkonganti@0 143 which is only effective with FASTQ input.
kkonganti@0 144 Default: 0
kkonganti@0 145
kkonganti@0 146 --kraken2_report_zero_counts : Report counts for ALL taxa, even if counts
kkonganti@0 147 are zero. Default: false
kkonganti@0 148
kkonganti@0 149 --kraken2_report_minmizer_data : Report minimizer and distinct minimizer
kkonganti@0 150 count information in addition to normal
kkonganti@0 151 Kraken report. Default: false
kkonganti@0 152
kkonganti@0 153 --kraken2_use_names : Print scientific names instead of just
kkonganti@0 154 taxids. Default: true
kkonganti@0 155
kkonganti@0 156 --kraken2_extract_bug : Extract the reads or contigs beloging to
kkonganti@0 157 this bug. Default: Escherichia coli
kkonganti@0 158
kkonganti@0 159 --centrifuge_x : Absolute path to centrifuge database.
kkonganti@0 160 Default: /hpc/db/centrifuge/2022-04-12/ab
kkonganti@0 161
kkonganti@0 162 --centrifuge_save_unaligned : Save SINGLE-END reads that did not align.
kkonganti@0 163 For PAIRED-END reads, save read pairs that
kkonganti@0 164 did not align concordantly. Default: false
kkonganti@0 165
kkonganti@0 166 --centrifuge_save_aligned : Save SINGLE-END reads that aligned. For
kkonganti@0 167 PAIRED-END reads, save read pairs that
kkonganti@0 168 aligned concordantly. Default: false
kkonganti@0 169
kkonganti@0 170 --centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default:
kkonganti@0 171 false
kkonganti@0 172
kkonganti@0 173 --centrifuge_extract_bug : Extract this bug from centrifuge results.
kkonganti@0 174 Default: Escherichia coli
kkonganti@0 175
kkonganti@0 176 --centrifuge_ignore_quals : Treat all quality values as 30 on Phred
kkonganti@0 177 scale. Default: false
kkonganti@0 178
kkonganti@0 179 --spades_isolate : This flag is highly recommended for high-
kkonganti@0 180 coverage isolate and multi-cell data.
kkonganti@0 181 Defaut: false
kkonganti@0 182
kkonganti@0 183 --spades_sc : This flag is required for MDA (single-cell)
kkonganti@0 184 data. Default: false
kkonganti@0 185
kkonganti@0 186 --spades_meta : This flag is required for metagenomic data.
kkonganti@0 187 Default: true
kkonganti@0 188
kkonganti@0 189 --spades_bio : This flag is required for biosytheticSPAdes
kkonganti@0 190 mode. Default: false
kkonganti@0 191
kkonganti@0 192 --spades_corona : This flag is required for coronaSPAdes mode.
kkonganti@0 193 Default: false
kkonganti@0 194
kkonganti@0 195 --spades_rna : This flag is required for RNA-Seq data.
kkonganti@0 196 Default: false
kkonganti@0 197
kkonganti@0 198 --spades_plasmid : Runs plasmidSPAdes pipeline for plasmid
kkonganti@0 199 detection. Default: false
kkonganti@0 200
kkonganti@0 201 --spades_metaviral : Runs metaviralSPAdes pipeline for virus
kkonganti@0 202 detection. Default: false
kkonganti@0 203
kkonganti@0 204 --spades_metaplasmid : Runs metaplasmidSPAdes pipeline for plasmid
kkonganti@0 205 detection in metagenomics datasets. Default:
kkonganti@0 206 false
kkonganti@0 207
kkonganti@0 208 --spades_rnaviral : This flag enables virus assembly module
kkonganti@0 209 from RNA-Seq data. Default: false
kkonganti@0 210
kkonganti@0 211 --spades_iontorrent : This flag is required for IonTorrent data.
kkonganti@0 212 Default: false
kkonganti@0 213
kkonganti@0 214 --spades_only_assembler : Runs only the SPAdes assembler module (
kkonganti@0 215 without read error correction).Default:
kkonganti@0 216 false
kkonganti@0 217
kkonganti@0 218 --spades_careful : Tries to reduce the number of mismatches
kkonganti@0 219 and short indels in the assembly. Default:
kkonganti@0 220 false
kkonganti@0 221
kkonganti@0 222 --spades_cov_cutoff : Coverage cutoff value (a positive float
kkonganti@0 223 number). Default: false
kkonganti@0 224
kkonganti@0 225 --spades_k : List of k-mer sizes (must be odd and less
kkonganti@0 226 than 128). Default: false
kkonganti@0 227
kkonganti@0 228 --spades_hmm : Directory with custom hmms that replace the
kkonganti@0 229 default ones (very rare). Default: false
kkonganti@0 230
kkonganti@0 231 --serotypefinder_run : Run SerotypeFinder tool. Default: true
kkonganti@0 232
kkonganti@0 233 --serotypefinder_x : Generate extended output files. Default:
kkonganti@0 234 true
kkonganti@0 235
kkonganti@0 236 --serotypefinder_db : Path to SerotypeFinder databases. Default: /
kkonganti@0 237 hpc/db/serotypefinder/2.0.2
kkonganti@0 238
kkonganti@0 239 --serotypefinder_min_threshold : Minimum percent identity (in float)
kkonganti@0 240 required for calling a hit. Default: 0.85
kkonganti@0 241
kkonganti@0 242 --serotypefinder_min_cov : Minumum percent coverage (in float)
kkonganti@0 243 required for calling a hit. Default: 0.80
kkonganti@0 244
kkonganti@0 245 --seqsero2_run : Run SeqSero2 tool. Default: false
kkonganti@0 246
kkonganti@0 247 --seqsero2_t : '1' for interleaved paired-end reads, '2'
kkonganti@0 248 for separated paired-end reads, '3' for
kkonganti@0 249 single reads, '4' for genome assembly, '5'
kkonganti@0 250 for nanopore reads (fasta/fastq). Default:
kkonganti@0 251 4
kkonganti@0 252
kkonganti@0 253 --seqsero2_m : Which workflow to apply, 'a'(raw reads
kkonganti@0 254 allele micro-assembly), 'k'(raw reads and
kkonganti@0 255 genome assembly k-mer). Default: k
kkonganti@0 256
kkonganti@0 257 --seqsero2_c : SeqSero2 will only output serotype
kkonganti@0 258 prediction without the directory containing
kkonganti@0 259 log files. Default: false
kkonganti@0 260
kkonganti@0 261 --seqsero2_s : SeqSero2 will not output header in
kkonganti@0 262 SeqSero_result.tsv. Default: false
kkonganti@0 263
kkonganti@0 264 --mlst_run : Run MLST tool. Default: true
kkonganti@0 265
kkonganti@0 266 --mlst_minid : DNA %identity of full allelle to consider '
kkonganti@0 267 similar' [~]. Default: 95
kkonganti@0 268
kkonganti@0 269 --mlst_mincov : DNA %cov to report partial allele at all [?].
kkonganti@0 270 Default: 10
kkonganti@0 271
kkonganti@0 272 --mlst_minscore : Minumum score out of 100 to match a scheme.
kkonganti@0 273 Default: 50
kkonganti@0 274
kkonganti@0 275 --abricate_run : Run ABRicate tool. Default: true
kkonganti@0 276
kkonganti@0 277 --abricate_minid : Minimum DNA %identity. Defaut: 90
kkonganti@0 278
kkonganti@0 279 --abricate_mincov : Minimum DNA %coverage. Defaut: 80
kkonganti@0 280
kkonganti@0 281 --abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/
kkonganti@0 282 abricate/1.0.1/db
kkonganti@0 283
kkonganti@0 284 Help options :
kkonganti@0 285
kkonganti@0 286 --help : Display this message.
kkonganti@0 287 ```
kkonganti@0 288
kkonganti@0 289 ### **PRE ALPHA**
kkonganti@0 290
kkonganti@0 291 ---
kkonganti@0 292 This modular structure and flow is still in rapid development and may change
kkonganti@0 293 depending on assessment of various computational topics and other considerations