nf-core/kmermaid

Only a parameter added to avoid warning as per nf-core

Path to Local or s3 directories containing R1,R2.fastq.gz files, separated by commas.

Path to Local or s3 directories of single-end read files, separated by commas.

CSV file with columns id, read1, read2 for each sample

CSV file with columns id, read1, for each sample

Path to FASTA sequence files. Can be semi-colon-separated.

Path to protein fasta inputs.

Path to bam input.

Path to input tgz folder containing bam and bai files.

SRR, ERR, SRP IDs representing a project. Only compatible with Nextflow 19.03-edge or greater

Email address for completion summary.

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

Number of hashes to use for making the sketches. Mutually exclusive with —sketch_num_hashes_log2

Which log2 sketch sizes to use. Multiple are separated by commas. Mutually exclusive with —sketch_num_hashes

Observe every 1/N hashes per sample, rather than a flat rate of N hashes per sample. This way, the number of hashes scales by the sequencing depth. Mutually exclusive with —sketch_scaled_log2

Same as —sketch_scaled, but instead of specifying the true number of hashes, specify the power to take 2 to. Mutually exlusive with —sketch_scaled

Track abundance of each hashed k-mer, could be useful for cancer RNA-seq or ATAC-seq analyses

If provided, use SKA to compute split k-mer sketches instead of sourmash to compute k-mer sketches

Which nucleotide k-mer sizes to use. Multiple are separated by commas

dna,protein,dayhoff

Integer value to subsample reads from input fastq files

Path to a well-curated fasta file of protein sequences. Used to filter for coding reads

K-mer size to use for translating RNA into protein, which is good for ‘protein’. If using dayhoff, suggest 15

Which molecular encoding to use for translating.If your reference proteome is quite different from your species of interest, suggest using dayhoff

Minimum fraction of overlapping translated k-mers from the read to match to the reference.

Maximum table size for bloom filter creation

If on, removes ribosomal RNA

Save non ribosomal rna reads if true

Path to rrna database manifest txt file

A barcode is only considered a valid barcode read and its signature is written if number of umis are greater than tenx_min_umi_per_cell

Number of alignment to contain in each sharded bam file

For bam files, Optional absolute path to a .tsv barcodes file if the input is unfiltered 10x bam file

For bam files, Optional absolute path to a .tsv Tab-separated file mapping 10x barcode name to new name, e.g. with channel or cell annotation label

For bam files, Csv file name relative to outdir/barcode_metadata to write number of reads and number of umis per barcode. This csv file is empty with just header when the tenx_min_umi_per_cell is zero i.e Reads and umis per barcode are calculated only when the barcodes are filtered based on tenx_min_umi_per_cell

Path to single barcode save the fastas inside the output directory where the results will be saved.

10x sam tags

10x Cell pattern

10x UMI pattern

Skip fastp trimming of reads

Skip sourmash compute.

Skip sourmash compare.

Skip MultiQC.