Workflow Steps and Code Snippets

162 tagged steps and code snippets that match keyword Quant

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data (Version 1)

"""

kallisto quant -i $index $input_reads -t $task.cpus -o ./
cp ./abundance.tsv abudance.tsv   
"""

NextFlow Quant kallisto From line 45 of local/kallisto.nf

A Snakemake workflow to process paired-end RNA-Seq data.

shell:
    """
    salmon quant -i {input.index} -l A -1 {input.r1} -2 {input.r2} -o {output} --validateMappings --gcBias --seqBias --writeUnmappedNames --writeMappings={output.mappings} -p {threads} --numBootstraps 100
    """

SnakeMake Quant Salmon From line 49 of rules/06a_salmon.smk

shell:
    '''
    salmon quant -t {input.tcp} -l A -a {input.bam} -o {output} --gcBias --seqBias --writeUnmappedNames -p {threads} -g {input.gtf} --numBootstraps 100
    '''

SnakeMake Quant Salmon From line 91 of rules/06a_salmon.smk

shell:
    "kallisto quant --threads {threads} -i {input.idx} -o {output} --gtf {input.gtf} "
    "{params.extra} {input.r1} {input.r2} 2> {log}"

SnakeMake Quant kallisto From line 29 of rules/06b_kallisto.smk

Processing sorted cells from BC1 that have been bulkrnaseq'd

shell:
    """
    kallisto quant -i {input.idx} -o {output} -t {threads} \
        {params.strand} {params.single} {params.frag_length} {params.frag_sd} \
        {params.fqs} &> >(tee {log})
    """

SnakeMake Quant kallisto From line 120 of main/Snakefile

shell:
    """
    salmon quant -i {input.idx} -l A {params.fqs} -p {threads} -o {output}
    """

SnakeMake Quant Salmon From line 140 of main/Snakefile

A metatranscriptomic pipeline optimized for the study of microeukaryotes. (v1.0)

shell:
    """
    salmon index -t {input.fastafile} -i {params.indexname} -k {params.kval} 2> {log.err} 1> {log.out}
    salmon quant -i {params.indexname} -l {params.libtype} -1 {input.left} -2 {input.right} --validateMappings -o {params.outdir} 2>> {log.err} 1>> {log.out}
    """

SnakeMake Quant Salmon From line 50 of rules/salmon-snake.smk

shell:
    """
    salmon index -t {input.fastafile} -i {params.indexname} -k {params.kval} 2> {log.err} 1> {log.out}
    salmon quant -i {params.indexname} -l {params.libtype} -1 {input.left} -2 {input.right} --validateMappings -o {params.outdir} 2>> {log.err} 1>> {log.out}
    """

SnakeMake Quant Salmon From line 72 of rules/salmon-snake.smk

shell:
    """
    salmon index -t {input.assemblyfile} -i {params.indexname} -k {params.kval} 2> {log.err} 1> {log.out}
    salmon quant -i {params.indexname} -l {params.libtype} -1 {input.left} -2 {input.right} --validateMappings -o {params.outdir} 2>> {log.err} 1>> {log.out}
    """

SnakeMake Quant Salmon From line 96 of rules/salmon-snake.smk

shell:
    """
    salmon index -t {input.assemblyfile} -i {params.indexname} -k {params.kval} 2> {log.err} 1> {log.out}
    salmon quant -i {params.indexname} -l {params.libtype} -1 {input.left} -2 {input.right} --validateMappings -o {params.outdir} 2>> {log.err} 1>> {log.out}
    """