quantify_pseudo_alignment

Perform quantification with Salmon or Kallisto to produce count tables and SummarizedExperiment objects

rnaseqquantificationkallistosalmon

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/quantify_pseudo_alignment

Description

Perform quantification with Salmon or Kallisto to produce count tables and SummarizedExperiment objects

Input

name

description

pattern

`samplesheet`

Sample sheet, to be baked into the colData of summarizedexperiment
objects.

*.{csv,tsv}

`reads`

Channel with input FastQ files of size 1 and 2 for single-end and
paired-end data, respectively. OR a transcriptome-level BAM file if
running Salmon in alignment mode.

`index`

Channel of [ val(meta2), index ]: Salmon or Kallisto index in the
tool-appropriate form.

`transcript_fasta`

Channel with the transcriptome in FASTA format. Required when running
Salmon in alignment mode.

`gtf`

Channel with features in GTF format. Passed to pseudoaligners and used
to generate transcript/ gene mappings.

`gtf_id_attribute`

Attribute in GTF file corresponding to the gene identifier.

`gtf_extra_attribute`

GTF alternative gene attribute (e.g. gene_name)

`pseudo_aligner`

Pseudoaligner, kallisto or salmon.

`kallisto_quant_fraglen`

Estimated fragment length. Required if running Kallisto with
single-ended reads.

`kallisto_quant_fraglen_sd`

Estimated standard error for fragment length required by Kallisto in
single-end mode.

`skip_merge`

Skip cross-sample merging. When true, runs tximport per-sample
instead of collecting all samples, and skips SummarizedExperiment
creation. Useful for very large cohorts.

Output

name

description

pattern

`results`

Channel containing sample-wise results directories from the
pseudoaligner.

`multiqc`

Channel containing those pseudoaligner outputs readable by MultiQC for
passing to workflow-level reporting.

`tx2gene`

Transcript-to-gene mapping file generated from the GTF.

*.tx2gene.tsv

`tx2gene_augmented`

tx2gene mapping table actually used by tximport, equal to the input
tx2gene with self-mappings appended for any transcripts present in the
quantification output but missing from the input. Use this file (not
tx2gene) to reproduce the published gene-level outputs from the
per-sample quantification files.

*tx2gene_augmented.tsv

`tpm_gene`

Gene-level matrix of abundance values in TPM.

*.gene_tpm.tsv

`counts_gene`

Gene-level matrix of unadjusted estimated counts from tximport
(countsFromAbundance = 'no').

*.gene_counts.tsv

`lengths_gene`

Gene-level matrix of length values for modelling in downstream
analysis.

gene_lengths.tsv

`counts_gene_length_scaled`

Gene-level matrix of estimated counts, generated from abundance (TPM)
values by scaling to library size, additionally scaled using the
average transcript length, averaged over samples and to library size,
using tximport countsFromAbundance = 'lengthScaledTPM'.

*.gene_counts_length_scaled.tsv

`counts_gene_scaled`

Gene-level matrix of estimated counts, generated from abundance (TPM)
values by scaling to library size with tximport countsFromAbundance = 'scaledTPM'.

*.gene_counts_length_scaled.tsv

`tpm_transcript`

Transcript-level matrix of abundance values in TPM.

*.transcript_tpm.tsv

`counts_transcript`

Transcript-level matrix of unadjusted estimated counts from tximport
(countsFromAbundance = 'no').

*.transcript_counts.tsv

`lengths_transcript`

Transcript-level matrix of length values for modelling in downstream
analysis.

transcript_lengths.tsv

`merged_gene_rds_unified`

Serialised SummarizedExperiment object containing gene level
abundance, count, and length matrices generated from tximport.

*.rds

`merged_transcript_rds_unified`

Serialised SummarizedExperiment object containing transcript level
abundance, count, and length matrices generated from tximport.