workflows/runner

Description

Opinionated runner for the bulk RNA-seq pipeline. Wraps the layout-agnostic
bulk_rnaseq workflow and adds run identity (project/experiment IDs), an S3-style
output hierarchy with per-tool subdirectories, an early Kallisto preview
published to a separate root while STAR is still running, and a params.yaml
snapshot for reproducibility.

Type

nextflow_script

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
strandedness: [ "reverse" ]  
genome_sa_index_nbases: [ 14 ]  
id: "run"  
fastqc_html_1: "$id.$key.fastqc_html_1"  
fastqc_html_2: "$id.$key.fastqc_html_2"  
fastqc_zip_1: "$id.$key.fastqc_zip_1"  
fastqc_zip_2: "$id.$key.fastqc_zip_2"  
fastqc_trim_html_1: "$id.$key.fastqc_trim_html_1"  
fastqc_trim_html_2: "$id.$key.fastqc_trim_html_2"  
fastqc_trim_zip_1: "$id.$key.fastqc_trim_zip_1"  
fastqc_trim_zip_2: "$id.$key.fastqc_trim_zip_2"  
trim_reads_1: "$id.$key.trim_reads_1"  
trim_reads_2: "$id.$key.trim_reads_2"  
trim_log_r1: "$id.$key.trim_log_r1"  
trim_log_r2: "$id.$key.trim_log_r2"  
genome_bam: "$id.$key.genome_bam"  
transcriptome_bam: "$id.$key.transcriptome_bam"  
star_log: "$id.$key.star_log"  
kallisto_output: "$id.$key.kallisto_output"  
salmon_output: "$id.$key.salmon_output"  
salmon_quant_sf: "$id.$key.salmon_quant_sf"  
qualimap_output: "$id.$key.qualimap_output"  
multiqc_report: "$id.$key.multiqc_report"  
run_params: "$id.$key.run_params"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/bulk-rnaseq.git \  
  -revision v0.2.0 \  
  -main-script target/nextflow/workflows/runner/main.nf \  
  -params-file params.yaml

Input arguments

Name	Type & Properties	Description
--input_fastq_1	file required multiple	R1 FASTQ file (or single-end FASTQ).
--input_fastq_2	file multiple	R2 FASTQ file for paired-end reads. Omit for single-end.
--strandedness	string	Library strandedness.

Name

Type & Properties

--input_fastq_1

file

required

multiple

--input_fastq_2

file

multiple

--strandedness

string

Reference arguments

Name	Type & Properties	Description
--genome_fasta	file required	Reference genome FASTA file (plain or gzipped).
--gtf	file required	Gene annotation GTF file (plain or gzipped).
--transcript_fasta	file required	Transcript FASTA file for Kallisto and Salmon alignment mode.
--genome_sa_index_nbases	integer	STAR genomeSAindexNbases. Default (14) is correct for full genomes. Use 7 for small test genomes.
--star_index	file	Pre-built STAR genome index directory. If provided, index generation is skipped.
--kallisto_index	file	Pre-built Kallisto index file. If provided, index generation is skipped.

Name

Type & Properties

--genome_fasta

file

required

--gtf

file

required

--transcript_fasta

file

required

--genome_sa_index_nbases

integer

--star_index

file

--kallisto_index

file

Trimming options

Name	Type & Properties	Description
--skip_trim	boolean_true	Skip adapter trimming with TrimGalore. Raw reads are passed directly to alignment.

Name

Type & Properties

--skip_trim

boolean_true

Single-end options

Name	Type & Properties	Description
--fragment_length	double	Estimated average fragment length (required for single-end Kallisto).
--sd	double	Estimated standard deviation of fragment length (required for single-end Kallisto).

Name

Type & Properties

--fragment_length

double

--sd

double

Metadata arguments

Name	Type & Properties	Description
--id	string	Unique identifier for the sample.
--run_id	string	Identifier for the sequencing run.
--project_id	string required	Project ID. Determines the top level of the output hierarchy.
--experiment_id	string required	Experiment ID. Determines the second level of the output hierarchy.

Name

Type & Properties

--id

string

--run_id

string

--project_id

string

required

--experiment_id

string

required

Publish arguments

Name	Type & Properties	Description
--early_publish_dir	string	Root directory for the early Kallisto preview, published while STAR is still running. The preview lands at <early_publish_dir>/<project_id>/<experiment_id>/data_processed/<date>_rnaseq_<version>/kallisto/<id>.kallisto_quant, carrying the same date and version as the final results. Defaults to the launch-level --publish_dir, which puts the preview alongside the results tree.

Name

Type & Properties

--early_publish_dir

string

Output arguments

Name	Type & Properties	Description
--fastqc_html_1	file output	FastQC HTML report on raw read 1.
--fastqc_html_2	file output	FastQC HTML report on raw read 2 (paired-end only).
--fastqc_zip_1	file output	FastQC zip archive on raw read 1.
--fastqc_zip_2	file output	FastQC zip archive on raw read 2 (paired-end only).
--fastqc_trim_html_1	file output	FastQC HTML report on trimmed read 1.
--fastqc_trim_html_2	file output	FastQC HTML report on trimmed read 2 (paired-end only).
--fastqc_trim_zip_1	file output	FastQC zip archive on trimmed read 1.
--fastqc_trim_zip_2	file output	FastQC zip archive on trimmed read 2 (paired-end only).
--trim_reads_1	file output	Trimmed r1 reads (or original r1 when --skip_trim is set).
--trim_reads_2	file output	Trimmed r2 reads for paired-end (or original r2 when --skip_trim is set).
--trim_log_r1	file output	TrimGalore trimming report for r1.
--trim_log_r2	file output	TrimGalore trimming report for r2 (paired-end only).
--genome_bam	file output	Coordinate-sorted genome BAM from STAR.
--transcriptome_bam	file output	Transcriptome-aligned BAM from STAR (input for Salmon).
--star_log	file output	STAR alignment log (Log.final.out).
--kallisto_output	file output	Kallisto pseudo-alignment output directory.
--salmon_output	file output	Salmon quantification output directory.
--salmon_quant_sf	file output	Salmon per-transcript counts file.
--qualimap_output	file output	Qualimap rnaseq_qc_results.txt file (exon coverage, 5'/3' bias).
--multiqc_report	file output	MultiQC HTML report aggregating all QC outputs.
--run_params	file output	Snapshot of the resolved run state for reproducibility.

Name

Type & Properties

--fastqc_html_1

file

output

--fastqc_html_2

file

output

--fastqc_zip_1

file

output

--fastqc_zip_2

file

output

--fastqc_trim_html_1

file

output

--fastqc_trim_html_2

file

output

--fastqc_trim_zip_1

file

output

--fastqc_trim_zip_2

file

output

--trim_reads_1

file

output

--trim_reads_2

file

output

--trim_log_r1

file

output

--trim_log_r2

file

output

--genome_bam

file

output

--transcriptome_bam

file

output

--star_log

file

output

--kallisto_output

file

output

--salmon_output

file

output

--salmon_quant_sf

file

output

--qualimap_output

file

output

--multiqc_report

file

output

--run_params

file

output