kkonganti@101: # CPIPES (CFSAN PIPELINES) kkonganti@101: kkonganti@101: ## The modular pipeline repository at CFSAN, FDA kkonganti@101: kkonganti@101: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**, kkonganti@101: mostly for bioinformatics data analysis at **CFSAN, FDA.** kkonganti@101: kkonganti@101: --- kkonganti@101: kkonganti@101: ### **centriflaken_hy** kkonganti@101: kkonganti@101: --- kkonganti@101: `centriflaken_hy` is a variant of the original `centriflaken` pipeline but for Illumina short reads either single-end or paired-end. kkonganti@101: kkonganti@101: #### Workflow Usage kkonganti@101: kkonganti@101: ```bash kkonganti@101: module load cpipes/0.4.0 kkonganti@101: kkonganti@101: cpipes --pipeline centriflaken_hy [options] kkonganti@101: ``` kkonganti@101: kkonganti@101: Example: Run the default `centriflaken_hy` pipeline with taxa of interest as *E. coli*. kkonganti@101: kkonganti@101: ```bash kkonganti@101: cd /hpc/scratch/$USER kkonganti@101: mkdir nf-cpipes kkonganti@101: cd nf-cpipes kkonganti@101: cpipes --pipeline centriflaken_hy --input /path/to/illumina/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov' kkonganti@101: ``` kkonganti@101: kkonganti@101: Example: Run the `centriflaken_hy` pipeline with taxa of interest as *Salmonella*. In this mode, `SerotypeFinder` tool will be replaced with `SeqSero2` tool. kkonganti@101: kkonganti@101: ```bash kkonganti@101: cd /hpc/scratch/$USER kkonganti@101: mkdir nf-cpipes kkonganti@101: cd nf-cpipes kkonganti@101: 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@101: ``` kkonganti@101: kkonganti@101: #### `centriflaken_hy` Help kkonganti@101: kkonganti@101: ```text kkonganti@101: [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help kkonganti@101: N E X T F L O W ~ version 21.12.1-edge kkonganti@101: Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [soggy_curie] - revision: 72db279311 kkonganti@101: ================================================================================ kkonganti@101: (o) kkonganti@101: ___ _ __ _ _ __ ___ ___ kkonganti@101: / __|| '_ \ | || '_ \ / _ \/ __| kkonganti@101: | (__ | |_) || || |_) || __/\__ \ kkonganti@101: \___|| .__/ |_|| .__/ \___||___/ kkonganti@101: | | | | kkonganti@101: |_| |_| kkonganti@101: -------------------------------------------------------------------------------- kkonganti@101: A collection of modular pipelines at CFSAN, FDA. kkonganti@101: -------------------------------------------------------------------------------- kkonganti@101: Name : CPIPES kkonganti@101: Author : Kranti.Konganti@fda.hhs.gov kkonganti@101: Version : 0.4.0 kkonganti@101: Center : CFSAN, FDA. kkonganti@101: ================================================================================ kkonganti@101: kkonganti@101: Workflow : centriflaken_hy kkonganti@101: kkonganti@101: Author : Kranti.Konganti@fda.hhs.gov kkonganti@101: kkonganti@101: Version : 0.4.0 kkonganti@101: kkonganti@101: kkonganti@101: Usage : cpipes --pipeline centriflaken_hy [options] kkonganti@101: kkonganti@101: kkonganti@101: Required : kkonganti@101: kkonganti@101: --input : Absolute path to directory containing FASTQ kkonganti@101: files. The directory should contain only kkonganti@101: FASTQ files as all the files within the kkonganti@101: mentioned directory will be read. Ex: -- kkonganti@101: input /path/to/fastq_pass kkonganti@101: kkonganti@101: --output : Absolute path to directory where all the kkonganti@101: pipeline outputs should be stored. Ex: -- kkonganti@101: output /path/to/output kkonganti@101: kkonganti@101: Other options : kkonganti@101: kkonganti@101: --metadata : Absolute path to metadata CSV file kkonganti@101: containing five mandatory columns: sample, kkonganti@101: fq1,fq2,strandedness,single_end. The fq1 kkonganti@101: and fq2 columns contain absolute paths to kkonganti@101: the FASTQ files. This option can be used in kkonganti@101: place of --input option. This is rare. Ex: -- kkonganti@101: metadata samplesheet.csv kkonganti@101: kkonganti@101: --fq_suffix : The suffix of FASTQ files (Unpaired reads kkonganti@101: or R1 reads or Long reads) if an input kkonganti@101: directory is mentioned via --input option. kkonganti@101: Default: _R1_001.fastq.gz kkonganti@101: kkonganti@101: --fq2_suffix : The suffix of FASTQ files (Paired-end reads kkonganti@101: or R2 reads) if an input directory is kkonganti@101: mentioned via --input option. Default: kkonganti@101: _R2_001.fastq.gz kkonganti@101: kkonganti@101: --fq_filter_by_len : Remove FASTQ reads that are less than this kkonganti@101: many bases. Default: 75 kkonganti@101: kkonganti@101: --fq_strandedness : The strandedness of the sequencing run. kkonganti@101: This is mostly needed if your sequencing kkonganti@101: run is RNA-SEQ. For most of the other runs, kkonganti@101: it is probably safe to use unstranded for kkonganti@101: the option. Default: unstranded kkonganti@101: kkonganti@101: --fq_single_end : SINGLE-END information will be auto- kkonganti@101: detected but this option forces PAIRED-END kkonganti@101: FASTQ files to be treated as SINGLE-END so kkonganti@101: only read 1 information is included in auto- kkonganti@101: generated samplesheet. Default: false kkonganti@101: kkonganti@101: --fq_filename_delim : Delimiter by which the file name is split kkonganti@101: to obtain sample name. Default: _ kkonganti@101: kkonganti@101: --fq_filename_delim_idx : After splitting FASTQ file name by using kkonganti@101: the --fq_filename_delim option, all kkonganti@101: elements before this index (1-based) will kkonganti@101: be joined to create final sample name. kkonganti@101: Default: 1 kkonganti@101: kkonganti@101: --seqkit_rmdup_run : Remove duplicate sequences using seqkit kkonganti@101: rmdup. Default: false kkonganti@101: kkonganti@101: --seqkit_rmdup_n : Match and remove duplicate sequences by kkonganti@101: full name instead of just ID. Defaut: false kkonganti@101: kkonganti@101: --seqkit_rmdup_s : Match and remove duplicate sequences by kkonganti@101: sequence content. Defaut: true kkonganti@101: kkonganti@101: --seqkit_rmdup_d : Save the duplicated sequences to a file. kkonganti@101: Defaut: false kkonganti@101: kkonganti@101: --seqkit_rmdup_D : Save the number and list of duplicated kkonganti@101: sequences to a file. Defaut: false kkonganti@101: kkonganti@101: --seqkit_rmdup_i : Ignore case while using seqkit rmdup. kkonganti@101: Defaut: false kkonganti@101: kkonganti@101: --seqkit_rmdup_P : Only consider positive strand (i.e. 5') kkonganti@101: when comparing by sequence content. Defaut: kkonganti@101: false kkonganti@101: kkonganti@101: --kraken2_db : Absolute path to kraken database. Default: / kkonganti@101: hpc/db/kraken2/standard-210914 kkonganti@101: kkonganti@101: --kraken2_confidence : Confidence score threshold which must be kkonganti@101: between 0 and 1. Default: 0.0 kkonganti@101: kkonganti@101: --kraken2_quick : Quick operation (use first hit or hits). kkonganti@101: Default: false kkonganti@101: kkonganti@101: --kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa- kkonganti@101: report. Default: false kkonganti@101: kkonganti@101: --kraken2_minimum_base_quality : Minimum base quality used in classification kkonganti@101: which is only effective with FASTQ input. kkonganti@101: Default: 0 kkonganti@101: kkonganti@101: --kraken2_report_zero_counts : Report counts for ALL taxa, even if counts kkonganti@101: are zero. Default: false kkonganti@101: kkonganti@101: --kraken2_report_minmizer_data : Report minimizer and distinct minimizer kkonganti@101: count information in addition to normal kkonganti@101: Kraken report. Default: false kkonganti@101: kkonganti@101: --kraken2_use_names : Print scientific names instead of just kkonganti@101: taxids. Default: true kkonganti@101: kkonganti@101: --kraken2_extract_bug : Extract the reads or contigs beloging to kkonganti@101: this bug. Default: Escherichia coli kkonganti@101: kkonganti@101: --centrifuge_x : Absolute path to centrifuge database. kkonganti@101: Default: /hpc/db/centrifuge/2022-04-12/ab kkonganti@101: kkonganti@101: --centrifuge_save_unaligned : Save SINGLE-END reads that did not align. kkonganti@101: For PAIRED-END reads, save read pairs that kkonganti@101: did not align concordantly. Default: false kkonganti@101: kkonganti@101: --centrifuge_save_aligned : Save SINGLE-END reads that aligned. For kkonganti@101: PAIRED-END reads, save read pairs that kkonganti@101: aligned concordantly. Default: false kkonganti@101: kkonganti@101: --centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default: kkonganti@101: false kkonganti@101: kkonganti@101: --centrifuge_extract_bug : Extract this bug from centrifuge results. kkonganti@101: Default: Escherichia coli kkonganti@101: kkonganti@101: --centrifuge_ignore_quals : Treat all quality values as 30 on Phred kkonganti@101: scale. Default: false kkonganti@101: kkonganti@101: --megahit_run : Run MEGAHIT assembler. Default: true kkonganti@101: kkonganti@101: --megahit_min_count : . Minimum multiplicity for filtering ( kkonganti@101: k_min+1)-mers. Defaut: false kkonganti@101: kkonganti@101: --megahit_k_list : Comma-separated list of kmer size. All kkonganti@101: values must be odd, in the range 15-255, kkonganti@101: increment should be <= 28. Ex: '21,29,39,59, kkonganti@101: 79,99,119,141'. Default: false kkonganti@101: kkonganti@101: --megahit_no_mercy : Do not add mercy k-mers. Default: false kkonganti@101: kkonganti@101: --megahit_bubble_level : . Intensity of bubble merging (0-2), 0 kkonganti@101: to disable. Default: false kkonganti@101: kkonganti@101: --megahit_merge_level : . Merge complex bubbles of length <= l* kkonganti@101: kmer_size and similarity >= s. Default: kkonganti@101: false kkonganti@101: kkonganti@101: --megahit_prune_level : . Strength of low depth pruning (0-3). kkonganti@101: Default: false kkonganti@101: kkonganti@101: --megahit_prune_depth : . Remove unitigs with avg k-mer depth kkonganti@101: less than this value. Default: false kkonganti@101: kkonganti@101: --megahit_low_local_ratio : . Ratio threshold to define low kkonganti@101: local coverage contigs. Default: false kkonganti@101: kkonganti@101: --megahit_max_tip_len : . remove tips less than this value [< kkonganti@101: int> * k]. Default: false kkonganti@101: kkonganti@101: --megahit_no_local : Disable local assembly. Default: false kkonganti@101: kkonganti@101: --megahit_kmin_1pass : Use 1pass mode to build SdBG of k_min. kkonganti@101: Default: false kkonganti@101: kkonganti@101: --megahit_preset : . Override a group of parameters. kkonganti@101: Valid values are meta-sensitive which kkonganti@101: enforces '--min-count 1 --k-list 21,29,39, kkonganti@101: 49,...,129,141', meta-large (large & kkonganti@101: complex metagenomes, like soil) which kkonganti@101: enforces '--k-min 27 --k-max 127 --k-step kkonganti@101: 10'. Default: meta-sensitive kkonganti@101: kkonganti@101: --megahit_mem_flag : . SdBG builder memory mode. 0: minimum; kkonganti@101: 1: moderate; 2: use all memory specified. kkonganti@101: Default: 2 kkonganti@101: kkonganti@101: --megahit_min_contig_len : . Minimum length of contigs to output. kkonganti@101: Default: false kkonganti@101: kkonganti@101: --spades_run : Run SPAdes assembler. Default: false kkonganti@101: kkonganti@101: --spades_isolate : This flag is highly recommended for high- kkonganti@101: coverage isolate and multi-cell data. kkonganti@101: Defaut: false kkonganti@101: kkonganti@101: --spades_sc : This flag is required for MDA (single-cell) kkonganti@101: data. Default: false kkonganti@101: kkonganti@101: --spades_meta : This flag is required for metagenomic data. kkonganti@101: Default: true kkonganti@101: kkonganti@101: --spades_bio : This flag is required for biosytheticSPAdes kkonganti@101: mode. Default: false kkonganti@101: kkonganti@101: --spades_corona : This flag is required for coronaSPAdes mode. kkonganti@101: Default: false kkonganti@101: kkonganti@101: --spades_rna : This flag is required for RNA-Seq data. kkonganti@101: Default: false kkonganti@101: kkonganti@101: --spades_plasmid : Runs plasmidSPAdes pipeline for plasmid kkonganti@101: detection. Default: false kkonganti@101: kkonganti@101: --spades_metaviral : Runs metaviralSPAdes pipeline for virus kkonganti@101: detection. Default: false kkonganti@101: kkonganti@101: --spades_metaplasmid : Runs metaplasmidSPAdes pipeline for plasmid kkonganti@101: detection in metagenomics datasets. Default: kkonganti@101: false kkonganti@101: kkonganti@101: --spades_rnaviral : This flag enables virus assembly module kkonganti@101: from RNA-Seq data. Default: false kkonganti@101: kkonganti@101: --spades_iontorrent : This flag is required for IonTorrent data. kkonganti@101: Default: false kkonganti@101: kkonganti@101: --spades_only_assembler : Runs only the SPAdes assembler module ( kkonganti@101: without read error correction). Default: kkonganti@101: false kkonganti@101: kkonganti@101: --spades_careful : Tries to reduce the number of mismatches kkonganti@101: and short indels in the assembly. Default: kkonganti@101: false kkonganti@101: kkonganti@101: --spades_cov_cutoff : Coverage cutoff value (a positive float kkonganti@101: number). Default: false kkonganti@101: kkonganti@101: --spades_k : List of k-mer sizes (must be odd and less kkonganti@101: than 128). Default: false kkonganti@101: kkonganti@101: --spades_hmm : Directory with custom hmms that replace the kkonganti@101: default ones (very rare). Default: false kkonganti@101: kkonganti@101: --serotypefinder_run : Run SerotypeFinder tool. Default: true kkonganti@101: kkonganti@101: --serotypefinder_x : Generate extended output files. Default: kkonganti@101: true kkonganti@101: kkonganti@101: --serotypefinder_db : Path to SerotypeFinder databases. Default: / kkonganti@101: hpc/db/serotypefinder/2.0.2 kkonganti@101: kkonganti@101: --serotypefinder_min_threshold : Minimum percent identity (in float) kkonganti@101: required for calling a hit. Default: 0.85 kkonganti@101: kkonganti@101: --serotypefinder_min_cov : Minumum percent coverage (in float) kkonganti@101: required for calling a hit. Default: 0.80 kkonganti@101: kkonganti@101: --seqsero2_run : Run SeqSero2 tool. Default: false kkonganti@101: kkonganti@101: --seqsero2_t : '1' for interleaved paired-end reads, '2' kkonganti@101: for separated paired-end reads, '3' for kkonganti@101: single reads, '4' for genome assembly, '5' kkonganti@101: for nanopore reads (fasta/fastq). Default: kkonganti@101: 4 kkonganti@101: kkonganti@101: --seqsero2_m : Which workflow to apply, 'a'(raw reads kkonganti@101: allele micro-assembly), 'k'(raw reads and kkonganti@101: genome assembly k-mer). Default: k kkonganti@101: kkonganti@101: --seqsero2_c : SeqSero2 will only output serotype kkonganti@101: prediction without the directory containing kkonganti@101: log files. Default: false kkonganti@101: kkonganti@101: --seqsero2_s : SeqSero2 will not output header in kkonganti@101: SeqSero_result.tsv. Default: false kkonganti@101: kkonganti@101: --mlst_run : Run MLST tool. Default: true kkonganti@101: kkonganti@101: --mlst_minid : DNA %identity of full allelle to consider ' kkonganti@101: similar' [~]. Default: 95 kkonganti@101: kkonganti@101: --mlst_mincov : DNA %cov to report partial allele at all [?]. kkonganti@101: Default: 10 kkonganti@101: kkonganti@101: --mlst_minscore : Minumum score out of 100 to match a scheme. kkonganti@101: Default: 50 kkonganti@101: kkonganti@101: --abricate_run : Run ABRicate tool. Default: true kkonganti@101: kkonganti@101: --abricate_minid : Minimum DNA %identity. Defaut: 90 kkonganti@101: kkonganti@101: --abricate_mincov : Minimum DNA %coverage. Defaut: 80 kkonganti@101: kkonganti@101: --abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/ kkonganti@101: abricate/1.0.1/db kkonganti@101: kkonganti@101: Help options : kkonganti@101: kkonganti@101: --help : Display this message. kkonganti@101: ``` kkonganti@101: kkonganti@101: ### **BETA** kkonganti@101: kkonganti@101: --- kkonganti@101: 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.