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

`meta`

Groovy Map containing study-level sample sheet information. e.g. [
id:‘SRP1234’ ].

`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`

Path to Salmon or Kallisto index in the tool-appropriate form.

`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.

`alignment_mode`

If running Salmon, run in alignment mode (true or false).

`lib_type`

String to override Salmon library type.

`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

`meta`

Groovy Map containing study-level sample sheet information. e.g. [
id:‘SRP1234’ ].

`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.

`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.

*.rds

quantify_pseudo_alignment

Description

Input

`meta`

`samplesheet`

`reads`

`index`

`gtf`

`gtf_id_attribute`

`gtf_extra_attribute`

`pseudo_aligner`

`alignment_mode`

`lib_type`

`kallisto_quant_fraglen`

`kallisto_quant_fraglen_sd`

`skip_merge`

Output

`meta`

`results`

`multiqc`

`tpm_gene`

`counts_gene`

`lengths_gene`

`counts_gene_length_scaled`

`counts_gene_scaled`

`tpm_transcript`

`counts_transcript`

`lengths_transcript`

`merged_gene_rds_unified`

`merged_transcript_rds_unified`

included in

included modules and subworkflows

maintainers

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