Tool to decompress input FASTQ file(s). If several FASTQ files are provided, they will be concatenated in the order that corresponds to files in input. Bash script's logic: - disable case sensitive glob check - check if root name of input file already include '.fastq' or '.fq' extension. If yes, set DEFAULT_EXT to \"\", otherwise use '.fastq' - check file type, decompress if needed - return 1, if file type is not recognized This script also works of input file doesn't have any extension at all

Tool to decompress input FASTQ file(s). If several FASTQ files are provided, they will be concatenated in the order that corresponds to files in input. Bash script's logic: - disable case sensitive glob check - check if root name of input file already include '.fastq' or '.fq' extension. If yes, set DEFAULT_EXT to \"\", otherwise use '.fastq' - check file type, decompress if needed - return 1, if file type is not recognized This script also works of input file doesn't have any extension at all

Builds a kallisto index, transcript-to-gene mapping and cDNA/mismatch FASTA files. If workflow_type is lamanno or nucleus tool will produce additional three outputs: - intron FASTA file - cDNA transcripts-to-capture TSV file - intron transcripts-to-capture TSV file Otherwise the correspondent outputs will be null.

Notes: --verbose was hardcoded --keep-tmp, -d, --overwrite doesn't make sense when running from container -f2, -c1 and -c2 are always appended to the basecommand regardless of workflow_type (makes cwl less complicate)

`annotation_gtf_file` input should have correct \"gene_id\" field.

To generate correct GTF from refgene annotations use: `docker run --rm -ti -v `pwd`:/tmp/ biowardrobe2/ucscuserapps:v358 /bin/bash -c \"cut -f 2- refGene.txt | genePredToGtf file stdin refgene.gtf\"` to generate a proper gtf file from `refGene.txt` downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GEN}/database/refGene.txt.gz

Compresses input directory to tar.gz

Uses kallisto to pseudoalign reads and bustools to quantify the data.

1. Generates BUS file from input fastq files 2. Sorts generated BUS file 3. Inspects sorted BUS file 4. Corrects barcodes in sorted BUS file 5. Sorts corrected BUS file 6. Generates count matrix from sorted barcode corrected BUS file

Notes: --verbose was hardcoded --keep-tmp, --overwrite doesn't make sense when running from container -o is used by default, so all outputs go to the current folder

Not implemented parameters: -w --tcc --dry-run --filter

Tool runs FastQC from Babraham Bioinformatics

Tool runs FastQC from Babraham Bioinformatics