workflows/bulk_rnaseq

Description

Bulk RNA-seq pipeline: FastQC (raw + trimmed) → TrimGalore → Kallisto pseudo-alignment
(preliminary quantification) running in parallel with STAR alignment → Salmon
quantification (alignment mode) + Qualimap coordinate-based QC → MultiQC.

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 ]  
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"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/bulk-rnaseq.git \  
  -revision v0.2.0 \  
  -main-script target/nextflow/workflows/bulk_rnaseq/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

Publish arguments

Name	Type & Properties	Description
--early_publish_prefix	string	Directory, relative to the early publish root, that the Kallisto preview is copied into as soon as kallisto_quant finishes - ahead of STAR. Runners pass a run-specific (dated) prefix here; a publishDir directive cannot read per-sample state, so this has to arrive as a regular argument. Defaults to "kallisto_early". The root itself is the launch-level --early_publish_dir, falling back to the publish dir; when neither is set the preview is skipped.

Name

Type & Properties

--early_publish_prefix

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 input state for this sample, for reproducibility. Runners that aggregate params across samples pass run_params=null to skip this per-sample dump.

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