kkonganti@105: # CPIPES (CFSAN PIPELINES) kkonganti@105: kkonganti@105: ## The modular pipeline repository at CFSAN, FDA kkonganti@105: kkonganti@105: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**, kkonganti@105: mostly for bioinformatics data analysis at **CFSAN, FDA.** kkonganti@105: kkonganti@105: --- kkonganti@105: kkonganti@105: ### **centriflaken_hy** kkonganti@105: kkonganti@105: --- kkonganti@105: `centriflaken_hy` is a variant of the original `centriflaken` pipeline but for Illumina short reads either single-end or paired-end. kkonganti@105: kkonganti@105: #### Workflow Usage kkonganti@105: kkonganti@105: ```bash kkonganti@105: module load cpipes/0.4.0 kkonganti@105: kkonganti@105: cpipes --pipeline centriflaken_hy [options] kkonganti@105: ``` kkonganti@105: kkonganti@105: Example: Run the default `centriflaken_hy` pipeline with taxa of interest as *E. coli*. kkonganti@105: kkonganti@105: ```bash kkonganti@105: cd /hpc/scratch/$USER kkonganti@105: mkdir nf-cpipes kkonganti@105: cd nf-cpipes kkonganti@105: cpipes --pipeline centriflaken_hy --input /path/to/illumina/fastq/dir --output /path/to/output --user_email 'Kranti.Konganti@fda.hhs.gov' kkonganti@105: ``` kkonganti@105: kkonganti@105: Example: Run the `centriflaken_hy` pipeline with taxa of interest as *Salmonella*. In this mode, `SerotypeFinder` tool will be replaced with `SeqSero2` tool. kkonganti@105: kkonganti@105: ```bash kkonganti@105: cd /hpc/scratch/$USER kkonganti@105: mkdir nf-cpipes kkonganti@105: cd nf-cpipes kkonganti@105: 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: ``` kkonganti@105: kkonganti@105: #### `centriflaken_hy` Help kkonganti@105: kkonganti@105: ```text kkonganti@105: [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help kkonganti@105: N E X T F L O W ~ version 21.12.1-edge kkonganti@105: Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [soggy_curie] - revision: 72db279311 kkonganti@105: ================================================================================ kkonganti@105: (o) kkonganti@105: ___ _ __ _ _ __ ___ ___ kkonganti@105: / __|| '_ \ | || '_ \ / _ \/ __| kkonganti@105: | (__ | |_) || || |_) || __/\__ \ kkonganti@105: \___|| .__/ |_|| .__/ \___||___/ kkonganti@105: | | | | kkonganti@105: |_| |_| kkonganti@105: -------------------------------------------------------------------------------- kkonganti@105: A collection of modular pipelines at CFSAN, FDA. kkonganti@105: -------------------------------------------------------------------------------- kkonganti@105: Name : CPIPES kkonganti@105: Author : Kranti.Konganti@fda.hhs.gov kkonganti@105: Version : 0.4.0 kkonganti@105: Center : CFSAN, FDA. kkonganti@105: ================================================================================ kkonganti@105: kkonganti@105: Workflow : centriflaken_hy kkonganti@105: kkonganti@105: Author : Kranti.Konganti@fda.hhs.gov kkonganti@105: kkonganti@105: Version : 0.4.0 kkonganti@105: kkonganti@105: kkonganti@105: Usage : cpipes --pipeline centriflaken_hy [options] kkonganti@105: kkonganti@105: kkonganti@105: Required : kkonganti@105: kkonganti@105: --input : Absolute path to directory containing FASTQ kkonganti@105: files. The directory should contain only kkonganti@105: FASTQ files as all the files within the kkonganti@105: mentioned directory will be read. Ex: -- kkonganti@105: input /path/to/fastq_pass kkonganti@105: kkonganti@105: --output : Absolute path to directory where all the kkonganti@105: pipeline outputs should be stored. Ex: -- kkonganti@105: output /path/to/output kkonganti@105: kkonganti@105: Other options : kkonganti@105: kkonganti@105: --metadata : Absolute path to metadata CSV file kkonganti@105: containing five mandatory columns: sample, kkonganti@105: fq1,fq2,strandedness,single_end. The fq1 kkonganti@105: and fq2 columns contain absolute paths to kkonganti@105: the FASTQ files. This option can be used in kkonganti@105: place of --input option. This is rare. Ex: -- kkonganti@105: metadata samplesheet.csv kkonganti@105: kkonganti@105: --fq_suffix : The suffix of FASTQ files (Unpaired reads kkonganti@105: or R1 reads or Long reads) if an input kkonganti@105: directory is mentioned via --input option. kkonganti@105: Default: _R1_001.fastq.gz kkonganti@105: kkonganti@105: --fq2_suffix : The suffix of FASTQ files (Paired-end reads kkonganti@105: or R2 reads) if an input directory is kkonganti@105: mentioned via --input option. Default: kkonganti@105: _R2_001.fastq.gz kkonganti@105: kkonganti@105: --fq_filter_by_len : Remove FASTQ reads that are less than this kkonganti@105: many bases. Default: 75 kkonganti@105: kkonganti@105: --fq_strandedness : The strandedness of the sequencing run. kkonganti@105: This is mostly needed if your sequencing kkonganti@105: run is RNA-SEQ. For most of the other runs, kkonganti@105: it is probably safe to use unstranded for kkonganti@105: the option. Default: unstranded kkonganti@105: kkonganti@105: --fq_single_end : SINGLE-END information will be auto- kkonganti@105: detected but this option forces PAIRED-END kkonganti@105: FASTQ files to be treated as SINGLE-END so kkonganti@105: only read 1 information is included in auto- kkonganti@105: generated samplesheet. Default: false kkonganti@105: kkonganti@105: --fq_filename_delim : Delimiter by which the file name is split kkonganti@105: to obtain sample name. Default: _ kkonganti@105: kkonganti@105: --fq_filename_delim_idx : After splitting FASTQ file name by using kkonganti@105: the --fq_filename_delim option, all kkonganti@105: elements before this index (1-based) will kkonganti@105: be joined to create final sample name. kkonganti@105: Default: 1 kkonganti@105: kkonganti@105: --seqkit_rmdup_run : Remove duplicate sequences using seqkit kkonganti@105: rmdup. Default: false kkonganti@105: kkonganti@105: --seqkit_rmdup_n : Match and remove duplicate sequences by kkonganti@105: full name instead of just ID. Defaut: false kkonganti@105: kkonganti@105: --seqkit_rmdup_s : Match and remove duplicate sequences by kkonganti@105: sequence content. Defaut: true kkonganti@105: kkonganti@105: --seqkit_rmdup_d : Save the duplicated sequences to a file. kkonganti@105: Defaut: false kkonganti@105: kkonganti@105: --seqkit_rmdup_D : Save the number and list of duplicated kkonganti@105: sequences to a file. Defaut: false kkonganti@105: kkonganti@105: --seqkit_rmdup_i : Ignore case while using seqkit rmdup. kkonganti@105: Defaut: false kkonganti@105: kkonganti@105: --seqkit_rmdup_P : Only consider positive strand (i.e. 5') kkonganti@105: when comparing by sequence content. Defaut: kkonganti@105: false kkonganti@105: kkonganti@105: --kraken2_db : Absolute path to kraken database. Default: / kkonganti@105: hpc/db/kraken2/standard-210914 kkonganti@105: kkonganti@105: --kraken2_confidence : Confidence score threshold which must be kkonganti@105: between 0 and 1. Default: 0.0 kkonganti@105: kkonganti@105: --kraken2_quick : Quick operation (use first hit or hits). kkonganti@105: Default: false kkonganti@105: kkonganti@105: --kraken2_use_mpa_style : Report output like Kraken 1's kraken-mpa- kkonganti@105: report. Default: false kkonganti@105: kkonganti@105: --kraken2_minimum_base_quality : Minimum base quality used in classification kkonganti@105: which is only effective with FASTQ input. kkonganti@105: Default: 0 kkonganti@105: kkonganti@105: --kraken2_report_zero_counts : Report counts for ALL taxa, even if counts kkonganti@105: are zero. Default: false kkonganti@105: kkonganti@105: --kraken2_report_minmizer_data : Report minimizer and distinct minimizer kkonganti@105: count information in addition to normal kkonganti@105: Kraken report. Default: false kkonganti@105: kkonganti@105: --kraken2_use_names : Print scientific names instead of just kkonganti@105: taxids. Default: true kkonganti@105: kkonganti@105: --kraken2_extract_bug : Extract the reads or contigs beloging to kkonganti@105: this bug. Default: Escherichia coli kkonganti@105: kkonganti@105: --centrifuge_x : Absolute path to centrifuge database. kkonganti@105: Default: /hpc/db/centrifuge/2022-04-12/ab kkonganti@105: kkonganti@105: --centrifuge_save_unaligned : Save SINGLE-END reads that did not align. kkonganti@105: For PAIRED-END reads, save read pairs that kkonganti@105: did not align concordantly. Default: false kkonganti@105: kkonganti@105: --centrifuge_save_aligned : Save SINGLE-END reads that aligned. For kkonganti@105: PAIRED-END reads, save read pairs that kkonganti@105: aligned concordantly. Default: false kkonganti@105: kkonganti@105: --centrifuge_out_fmt_sam : Centrifuge output should be in SAM. Default: kkonganti@105: false kkonganti@105: kkonganti@105: --centrifuge_extract_bug : Extract this bug from centrifuge results. kkonganti@105: Default: Escherichia coli kkonganti@105: kkonganti@105: --centrifuge_ignore_quals : Treat all quality values as 30 on Phred kkonganti@105: scale. Default: false kkonganti@105: kkonganti@105: --megahit_run : Run MEGAHIT assembler. Default: true kkonganti@105: kkonganti@105: --megahit_min_count : . Minimum multiplicity for filtering ( kkonganti@105: k_min+1)-mers. Defaut: false kkonganti@105: kkonganti@105: --megahit_k_list : Comma-separated list of kmer size. All kkonganti@105: values must be odd, in the range 15-255, kkonganti@105: increment should be <= 28. Ex: '21,29,39,59, kkonganti@105: 79,99,119,141'. Default: false kkonganti@105: kkonganti@105: --megahit_no_mercy : Do not add mercy k-mers. Default: false kkonganti@105: kkonganti@105: --megahit_bubble_level : . Intensity of bubble merging (0-2), 0 kkonganti@105: to disable. Default: false kkonganti@105: kkonganti@105: --megahit_merge_level : . Merge complex bubbles of length <= l* kkonganti@105: kmer_size and similarity >= s. Default: kkonganti@105: false kkonganti@105: kkonganti@105: --megahit_prune_level : . Strength of low depth pruning (0-3). kkonganti@105: Default: false kkonganti@105: kkonganti@105: --megahit_prune_depth : . Remove unitigs with avg k-mer depth kkonganti@105: less than this value. Default: false kkonganti@105: kkonganti@105: --megahit_low_local_ratio : . Ratio threshold to define low kkonganti@105: local coverage contigs. Default: false kkonganti@105: kkonganti@105: --megahit_max_tip_len : . remove tips less than this value [< kkonganti@105: int> * k]. Default: false kkonganti@105: kkonganti@105: --megahit_no_local : Disable local assembly. Default: false kkonganti@105: kkonganti@105: --megahit_kmin_1pass : Use 1pass mode to build SdBG of k_min. kkonganti@105: Default: false kkonganti@105: kkonganti@105: --megahit_preset : . Override a group of parameters. kkonganti@105: Valid values are meta-sensitive which kkonganti@105: enforces '--min-count 1 --k-list 21,29,39, kkonganti@105: 49,...,129,141', meta-large (large & kkonganti@105: complex metagenomes, like soil) which kkonganti@105: enforces '--k-min 27 --k-max 127 --k-step kkonganti@105: 10'. Default: meta-sensitive kkonganti@105: kkonganti@105: --megahit_mem_flag : . SdBG builder memory mode. 0: minimum; kkonganti@105: 1: moderate; 2: use all memory specified. kkonganti@105: Default: 2 kkonganti@105: kkonganti@105: --megahit_min_contig_len : . Minimum length of contigs to output. kkonganti@105: Default: false kkonganti@105: kkonganti@105: --spades_run : Run SPAdes assembler. Default: false kkonganti@105: kkonganti@105: --spades_isolate : This flag is highly recommended for high- kkonganti@105: coverage isolate and multi-cell data. kkonganti@105: Defaut: false kkonganti@105: kkonganti@105: --spades_sc : This flag is required for MDA (single-cell) kkonganti@105: data. Default: false kkonganti@105: kkonganti@105: --spades_meta : This flag is required for metagenomic data. kkonganti@105: Default: true kkonganti@105: kkonganti@105: --spades_bio : This flag is required for biosytheticSPAdes kkonganti@105: mode. Default: false kkonganti@105: kkonganti@105: --spades_corona : This flag is required for coronaSPAdes mode. kkonganti@105: Default: false kkonganti@105: kkonganti@105: --spades_rna : This flag is required for RNA-Seq data. kkonganti@105: Default: false kkonganti@105: kkonganti@105: --spades_plasmid : Runs plasmidSPAdes pipeline for plasmid kkonganti@105: detection. Default: false kkonganti@105: kkonganti@105: --spades_metaviral : Runs metaviralSPAdes pipeline for virus kkonganti@105: detection. Default: false kkonganti@105: kkonganti@105: --spades_metaplasmid : Runs metaplasmidSPAdes pipeline for plasmid kkonganti@105: detection in metagenomics datasets. Default: kkonganti@105: false kkonganti@105: kkonganti@105: --spades_rnaviral : This flag enables virus assembly module kkonganti@105: from RNA-Seq data. Default: false kkonganti@105: kkonganti@105: --spades_iontorrent : This flag is required for IonTorrent data. kkonganti@105: Default: false kkonganti@105: kkonganti@105: --spades_only_assembler : Runs only the SPAdes assembler module ( kkonganti@105: without read error correction). Default: kkonganti@105: false kkonganti@105: kkonganti@105: --spades_careful : Tries to reduce the number of mismatches kkonganti@105: and short indels in the assembly. Default: kkonganti@105: false kkonganti@105: kkonganti@105: --spades_cov_cutoff : Coverage cutoff value (a positive float kkonganti@105: number). Default: false kkonganti@105: kkonganti@105: --spades_k : List of k-mer sizes (must be odd and less kkonganti@105: than 128). Default: false kkonganti@105: kkonganti@105: --spades_hmm : Directory with custom hmms that replace the kkonganti@105: default ones (very rare). Default: false kkonganti@105: kkonganti@105: --serotypefinder_run : Run SerotypeFinder tool. Default: true kkonganti@105: kkonganti@105: --serotypefinder_x : Generate extended output files. Default: kkonganti@105: true kkonganti@105: kkonganti@105: --serotypefinder_db : Path to SerotypeFinder databases. Default: / kkonganti@105: hpc/db/serotypefinder/2.0.2 kkonganti@105: kkonganti@105: --serotypefinder_min_threshold : Minimum percent identity (in float) kkonganti@105: required for calling a hit. Default: 0.85 kkonganti@105: kkonganti@105: --serotypefinder_min_cov : Minumum percent coverage (in float) kkonganti@105: required for calling a hit. Default: 0.80 kkonganti@105: kkonganti@105: --seqsero2_run : Run SeqSero2 tool. Default: false kkonganti@105: kkonganti@105: --seqsero2_t : '1' for interleaved paired-end reads, '2' kkonganti@105: for separated paired-end reads, '3' for kkonganti@105: single reads, '4' for genome assembly, '5' kkonganti@105: for nanopore reads (fasta/fastq). Default: kkonganti@105: 4 kkonganti@105: kkonganti@105: --seqsero2_m : Which workflow to apply, 'a'(raw reads kkonganti@105: allele micro-assembly), 'k'(raw reads and kkonganti@105: genome assembly k-mer). Default: k kkonganti@105: kkonganti@105: --seqsero2_c : SeqSero2 will only output serotype kkonganti@105: prediction without the directory containing kkonganti@105: log files. Default: false kkonganti@105: kkonganti@105: --seqsero2_s : SeqSero2 will not output header in kkonganti@105: SeqSero_result.tsv. Default: false kkonganti@105: kkonganti@105: --mlst_run : Run MLST tool. Default: true kkonganti@105: kkonganti@105: --mlst_minid : DNA %identity of full allelle to consider ' kkonganti@105: similar' [~]. Default: 95 kkonganti@105: kkonganti@105: --mlst_mincov : DNA %cov to report partial allele at all [?]. kkonganti@105: Default: 10 kkonganti@105: kkonganti@105: --mlst_minscore : Minumum score out of 100 to match a scheme. kkonganti@105: Default: 50 kkonganti@105: kkonganti@105: --abricate_run : Run ABRicate tool. Default: true kkonganti@105: kkonganti@105: --abricate_minid : Minimum DNA %identity. Defaut: 90 kkonganti@105: kkonganti@105: --abricate_mincov : Minimum DNA %coverage. Defaut: 80 kkonganti@105: kkonganti@105: --abricate_datadir : ABRicate databases folder. Defaut: /hpc/db/ kkonganti@105: abricate/1.0.1/db kkonganti@105: kkonganti@105: Help options : kkonganti@105: kkonganti@105: --help : Display this message. kkonganti@105: ``` kkonganti@105: kkonganti@105: ### **BETA** kkonganti@105: kkonganti@105: --- kkonganti@105: 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.