Titan-gc SARS-CoV-2 Strain Characterization Workflow for Bioconda V.3

conda create -n titan-cli -c conda-forge -c bioconda titan-gc

[me@PC ~]$ conda activate titan-cli
(titan-cli) [me@PC ~]$ conda deactivate
[me@PC~]$

conda update conda

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

(titan-cli) [me@PC ~]$ titan-gc-prepare.py
usage: titan-gc-prepare [-h] [-f STR] [--fastq_separator STR]
                        [--fastq_pattern STR] [--pe1_pattern STR]
                        [--pe2_pattern STR] [-r] [--prefix STR] [--tsv]
                        [--pangolin_docker STR] [--params STR]
                        FASTQ_PATH WORKFLOW PRIMER

titan-gc-prepare - Read a directory and prepare a JSON for input to Titan GC

optional arguments:
  -h, --help            show this help message and exit

Titan-GC Prepare Parameters:
  FASTQ_PATH            Directory where FASTQ files are stored
  WORKFLOW              The Titan-GC workflow to use for analysis. Options:
                        clearlabs, illumina_pe, illumina_se, ont
  PRIMER                A file containing primers (bed format) used during
                        sequencing.
  -f STR, --fastq_ext STR
                        Extension of the FASTQs. Default: .fastq.gz
  --fastq_separator STR
                        Split FASTQ name on the last occurrence of the
                        separator. Default: _
  --fastq_pattern STR   Glob pattern to match FASTQs. Default: *.fastq.gz
  --pe1_pattern STR     Designates difference first set of paired-end reads.
                        Default: ([Aa]|[Rr]1|1) (R1, r1, 1, A, a)
  --pe2_pattern STR     Designates difference second set of paired-end reads.
                        Default: ([Bb]|[Rr]2|2) (R2, r2, 2, AB b)
  -r, --recursive       Directories will be traversed recursively
  --prefix STR          Replace the absolute path with a given string.
                        Default: Use absolute path
  --tsv                 Output FOFN as a TSV (Default JSON)

Optional Titan-GC Workflow Parameters:
  --pangolin_docker STR
                        Docker image used to run Pangolin (takes priority over
                        --params)
  --params STR          A JSON file containing parameter values

titan-gc-prepare.py ./reads_dir illumina_pe ./primer.bed > input.file

(titan-cli) [me@PC test_seq]$ titan-gc-prepare.py . illumina_pe /$PATH/arctic_V3_nCov-2019.bed > input.json
(titan-cli) [me@PC test_seq]$ cat input.json
{
    "titan_gc.samples": [
        {
            "sample": "SRR13422799",
            "titan_wf": "illumina_pe",
            "r1": "/$PATH/SRR13422799_1.fastq.gz",
            "r2": "/$PATH/SRR13422799_2.fastq.gz",
            "primers": "/$PATH/arctic_V3_nCov-2019.bed"
        }
    ]
}

(titan-cli) [me@PC test_seq]$ titan-gc-prepare.py . illumina_pe /$PATH/arctic_V3_nCov-2019.bed --tsv > input.txt
(titan-cli) [me@PC test_seq]$ cat input.txt
sample  titan_wf        r1      r2      primers
SRR13422799     illumina_pe     /$PATH/test_seq/SRR13422799_1.fastq.gz       /$PATH/test_seq/SRR13422799_2.fastq.gz        /$PATH/arctic_V3_nCov-2019.bed

(titan-cli) [me@PC ~]$ titan-gc --help
usage: titan-gc [-h] [-i STR] [--inputs STR] [-o STR] [--outdir STR] [--options STR] [--quiet]

titan-gc-cli - Run Titan GC on a set of samples.

required arguments:
  -i STR, --inputs STR  The JSON file to be used with Cromwell for inputs.
  -o STR, --outdir STR  Output directory to store the final results in.

optional arguments:
  -h, --help              Show this help message and exit
  --options STR           JSON file containing Cromwell options
  --profile STR           The backend profile to use [options: docker, singularity]
  --config STR            Custom backend profile to use
  --cromwell_jar STR      Path to cromwell.jar (Default use conda install)
  --quiet                 Silence all STDOUT from Cromwell and titan-gc-organize

titan-gc -i input.json -o titan-out --profile singularity

nextflow pull -hub gitlab -r main steamboat/titan-nf

(titan-cli) [me@PC ~]$ nextflow run -hub gitlab -r main steamboat/titan-nf --help
N E X T F L O W  ~  version 21.04.0
Launching `steamboat/titan-nf` [berserk_ekeblad] - revision: e36cccd145 [main]

Required Parameters:
    --samples FILE          File produced by titan-gc-prepare.py (--tsv used)

Optional Parameters:
    --titan_opts FILE       A JSON file with Titan GC parameters to use.
                                Default: Use Titan-GC's defaults

    --pangolin_docker STR   The pangolin docker image to use
                                Default: Use Titan-GC's defaults

    --profile STR           Profile for Titan GC to use
                                Options: docker or singularity
                                Default: singularity

    --outdir DIR            Directory to write results to
                                Default: ./

    --run_name STR          Name to use for the results folder
                                Default: titan-gc

nextflow run -hub gitlab -r main steamboat/titan-nf --samples input.txt

(titan-cli) [me@PC test_seq]$ nextflow run -hub gitlab -r main steamboat/titan-nf --samples input.txt
N E X T F L O W  ~  version 21.04.0
Launching `steamboat/titan-nf` [clever_mercator] - revision: 3af325405e [main]
executor >  local (2)
[6e/1c5eb5] process > titan_gc (SRR13422799) [100%] 1 of 1 ✔
[41/fccd35] process > merge_results          [100%] 1 of 1 ✔
Completed at: 16-Jul-2021 12:33:51
Duration    : 3m 59s
CPU hours   : 0.3
Succeeded   : 2

(titan-cli) [me@PC test_seq]$ nextflow run -hub gitlab -r main steamboat/titan-nf --samples input.txt -resume
N E X T F L O W  ~  version 21.04.0
Launching `steamboat/titan-nf` [ecstatic_bhabha] - revision: 3af325405e [main]
[6e/1c5eb5] process > titan_gc (SRR13422799) [100%] 1 of 1, cached: 1 ✔
[41/fccd35] process > merge_results          [100%] 1 of 1, cached: 1 ✔

titan-out
├── alignments
│   ├── SRR13422799.flagstat.txt
│   ├── SRR13422799.primertrim.sorted.bam
│   ├── SRR13422799.primertrim.sorted.bam.bai
│   └── SRR13422799.stats.txt
├── assemblies
│   └── SRR13422799.ivar.consensus.fasta
├── cromwell
│   ├── SRR13422799-metadata.json
│   ├── SRR13422799-stderr.txt
│   └── SRR13422799-stdout.txt
├── dehosted_reads
│   ├── SRR13422799_R1_dehosted.fastq.gz
│   └── SRR13422799_R2_dehosted.fastq.gz
├── kraken2_reports
│   ├── SRR13422799_dehosted_kraken2_report.txt
│   └── SRR13422799_kraken2_report.txt
├── nextclade
│   ├── SRR13422799.ivar.consensus.nextclade.auspice.json
│   ├── SRR13422799.ivar.consensus.nextclade.json
│   └── SRR13422799.ivar.consensus.nextclade.tsv
├── nf-info
│   ├── titan-report.html
│   ├── titan-report.html.1
│   ├── titan-timeline.html
│   ├── titan-timeline.html.1
│   ├── titan-trace.txt
│   ├── titan-trace.txt.1
│   └── titan-trace.txt.2
├── pangolin_reports
│   └── SRR13422799.pangolin_report.csv
├── results
│   ├── SRR13422799.json
│   └── SRR13422799.tsv
├── titan-results.json
├── titan-results.tsv
└── vadr_alerts
    └── SRR13422799.ivar.consensus.vadr.alt.list