nf-core/rnaseq

Path to comma-separated file containing information about the samples in the experiment.

Path to the output directory where the results will be saved.

File containing SRA/ENA/GEO identifiers one per line in order to download their associated FastQ files.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Only download metadata for public data database ids and don’t download the FastQ files.

Save FastQ files after merging re-sequenced libraries in the results directory.

Enable UMI-based read deduplication.

UMI pattern to use. Can be either ‘string’ (default) or ‘regex’.

The UMI barcode pattern to use e.g. ‘NNNNNN’ indicates that the first 6 nucleotides of the read are from the UMI.

If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory.

Enable the removal of reads derived from ribosomal RNA using SortMeRNA.

Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.

If this option is specified, intermediate FastQ files containing non-rRNA reads will be saved in the results directory.

Name of iGenomes reference.

Path to FASTA genome file.

Path to GTF annotation file.

Path to GFF3 annotation file.

Path to BED file containing gene intervals. This will be created from the GTF file if not specified.

Path to FASTA transcriptome file.

FASTA file to concatenate to genome FASTA file e.g. containing spike-in sequences.

Splice sites file required for HISAT2.

Path to directory or tar.gz archive for pre-built STAR index.

Path to directory or tar.gz archive for pre-built HISAT2 index.

Path to directory or tar.gz archive for pre-built RSEM index.

Path to directory or tar.gz archive for pre-built Salmon index.

Memory passed to HISAT2 build process.

Specify if your GTF annotation is in GENCODE format.

If generated by the pipeline save the BWA index in the results directory.

Instructs Trim Galore to remove bp from the 5’ end of read 1 (or single-end reads).

Instructs Trim Galore to remove bp from the 5’ end of read 2 (paired-end reads only).

Instructs Trim Galore to remove bp from the 3’ end of read 1 AFTER adapter/quality trimming has been performed.

Instructs Trim Galore to remove bp from the 3’ end of read 2 AFTER adapter/quality trimming has been performed.

Instructs Trim Galore to apply the —nextseq=X option, to trim based on quality after removing poly-G tails.

Skip the adapter trimming step.

Save the trimmed FastQ files in the results directory.

Specifies the alignment algorithm to use - available options are ‘star’, ‘star_rsem’ and ‘hisat2’.

Specifies the pseudo aligner to use - available options are ‘salmon’. Runs in addition to ‘—aligner’.

When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file.

Minimum percentage of uniquely mapped reads below which samples are removed from further processing.

Sequencing center information to be added to read group of BAM files.

Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.

Save the intermediate BAM files from the alignment step.

Skip picard MarkDuplicates step.

Skip all of the alignment-based processes within the pipeline.

‘—extraAtributes’ parameter passed to featureCounts.

Define the attribute type used to group features in the GTF file.

Define the attribute type used to group feature types in the GTF file.

By default, the pipeline assigns reads based on the ‘exon’ attribute within the GTF file.

Perform reference-guided de novo assembly of transcripts using StringTie i.e. dont restrict to those in GTF file.

Skip additional featureCounts process for biotype QC.

Skip featureCounts.

Specify the RSeQC modules to run.

Use vst transformation instead of rlog with DESeq2.

Skip bigWig file creation.

Skip StringTie.

Skip FastQC.

Skip Preseq.

Skip dupRadar.

Skip Qualimap.

Skip RSeQC.

Skip DESeq2 PCA and heatmap plotting.

Skip MultiQC.

Skip all QC steps except for MultiQC.