workflows/genome_alignment_and_quant

Description

A viash sub-workflow for genome alignment and quantification stage of nf-core/rnaseq pipeline.

Type

nextflow_script

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
star_ignore_sjdbgtf: [ false ]  
bam_csi_index: [ false ]  
umi_dedup_stats: [ false ]  
with_umi: [ false ]  
gtf_group_features: [ "gene_id" ]  
gtf_extra_attributes: [ "gene_name" ]  
aligner: [ "star_salmon" ]  
star_multiqc: "$id.$key.star_multiqc"  
genome_bam_sorted: "$id.$key.genome_bam_sorted"  
genome_bam_index: "$id.$key.genome_bam_index"  
genome_bam_stats: "$id.$key.genome_bam_stats"  
genome_bam_flagstat: "$id.$key.genome_bam_flagstat"  
genome_bam_idxstats: "$id.$key.genome_bam_idxstats"  
transcriptome_bam: "$id.$key.transcriptome_bam"  
transcriptome_bam_index: "$id.$key.transcriptome_bam_index"  
transcriptome_bam_stats: "$id.$key.transcriptome_bam_stats"  
transcriptome_bam_flagstat: "$id.$key.transcriptome_bam_flagstat"  
transcriptome_bam_idxstats: "$id.$key.transcriptome_bam_idxstats"  
quant_out_dir: "$id.$key.quant_out_dir"  
quant_results_file: "$id.$key.quant_results_file"  
salmon_multiqc: "$id.$key.salmon_multiqc"  
rsem_counts_gene: "$id.$key.rsem_counts_gene"  
counts_transcripts: "$id.$key.counts_transcripts"  
rsem_multiqc: "$id.$key.rsem_multiqc"  
bam_star_rsem: "$id.$key.bam_star_rsem"  
bam_genome_rsem: "$id.$key.bam_genome_rsem"  
bam_transcript_rsem: "$id.$key.bam_transcript_rsem"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/rnaseq.git \  
  -revision v0.1.0 \  
  -main-script target/nextflow/workflows/genome_alignment_and_quant/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--id	string required	ID of the sample.
--fastq_1 -i	file required	Path to the sample (or read 1 of paired end sample).
--fastq_2	file	Path to read 2 of the sample.
--strandedness	string	Sample strand-specificity. Must be one of unstranded, forward, or reverse
--gtf	file	GTF file
--transcript_fasta	file	Fasta file of the reference transcriptome.
--star_index	file	STAR index directory.
--star_ignore_sjdbgtf	boolean	When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file
--seq_platform	string	Sequencing platform.
--seq_center	string	Sequencing center.
--extra_star_align_args	string	Extra arguments to pass to STAR alignment command in addition to defaults defined by the pipeline.
--bam_csi_index	boolean	Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.
--umi_dedup_stats	boolean	Generate output stats when running "umi_tools dedup".
--with_umi	boolean	Enable UMI-based read deduplication.
--salmon_quant_libtype	string	Override Salmon library type inferred based on strandedness defined in meta object.
--extra_salmon_quant_args	string	Extra arguments to pass to salmon quant command in addition to defaults defined by the pipeline.
--gtf_group_features	string	Define the attribute type used to group features in the GTF file when running Salmon.
--gtf_extra_attributes	string	By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon.
--extra_rsem_calculate_expression_args	string	Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline.
--aligner	string	Specifies the alignment algorithm to use - available options are 'star_salmon', 'star_rsem' and 'hisat2'.
--rsem_index	file	Path to directory for pre-built RSEM index.
--salmon_index	file	Path to directory for pre-built Salmon index.

Name

Type & Properties

--id

string

required

--fastq_1

-i

file

required

--fastq_2

file

--strandedness

string

--gtf

file

--transcript_fasta

file

--star_index

file

--star_ignore_sjdbgtf

boolean

--seq_platform

string

--seq_center

string

--extra_star_align_args

string

--bam_csi_index

boolean

--umi_dedup_stats

boolean

--with_umi

boolean

--salmon_quant_libtype

string

--extra_salmon_quant_args

string

--gtf_group_features

string

--gtf_extra_attributes

string

--extra_rsem_calculate_expression_args

string

--aligner

string

--rsem_index

file

--salmon_index

file

Output

Name	Type & Properties	Description
--star_multiqc	file output
--genome_bam_sorted	file output
--genome_bam_index	file output
--genome_bam_stats	file output
--genome_bam_flagstat	file output
--genome_bam_idxstats	file output
--transcriptome_bam	file output
--transcriptome_bam_index	file output
--transcriptome_bam_stats	file output
--transcriptome_bam_flagstat	file output
--transcriptome_bam_idxstats	file output
--quant_out_dir	file output
--quant_results_file	file output
--salmon_multiqc	file output
--rsem_counts_gene	file output	Expression counts on gene level
--counts_transcripts	file output	Expression counts on transcript level
--rsem_multiqc	file output	RSEM statistics
--bam_star_rsem	file output	BAM file generated by STAR (optional)
--bam_genome_rsem	file output	Genome BAM file (optional)
--bam_transcript_rsem	file output	Transcript BAM file (optional)

Name

Type & Properties

--star_multiqc

file

output

--genome_bam_sorted

file

output

--genome_bam_index

file

output

--genome_bam_stats

file

output

--genome_bam_flagstat

file

output

--genome_bam_idxstats

file

output

--transcriptome_bam

file

output

--transcriptome_bam_index

file

output

--transcriptome_bam_stats

file

output

--transcriptome_bam_flagstat

file

output

--transcriptome_bam_idxstats

file

output

--quant_out_dir

file

output

--quant_results_file

file

output

--salmon_multiqc

file

output

--rsem_counts_gene

file

output

--counts_transcripts

file

output

--rsem_multiqc

file

output

--bam_star_rsem

file

output

--bam_genome_rsem

file

output

--bam_transcript_rsem

file

output