2
$\begingroup$

I have a problem with nextflow -resume

Here is my script :

Reads_ch = Channel.fromSRA(params.ids, apiKey: params.apikey)
         .flatMap { left, right ->
            def SRRCode = left
            switch(right) {
                case { right.getClass() == java.util.ArrayList && right.size() == 2 }:
                    def forward = right[0]
                    def reverse = right[1]
                    return [tuple(SRRCode.concat("_1"), forward), tuple(SRRCode.concat("_2"), reverse)]

                case { right.getClass() == java.util.ArrayList && right.size() == 3 }:
                    def forward = right[1]
                    def reverse = right[2]
                    return [tuple(SRRCode.concat("_1"), forward), tuple(SRRCode.concat("_2"), reverse)]

                case right.getClass() == nextflow.file.http.XPath:
                    def sequence = right
                    return [tuple(SRRCode, sequence)]
            }
      }

process Unzip {
    tag "Unzip $fileCode reads files using unpigz"
    maxForks params.threads
    cpus params.threads_unzip

    input:
    set fileCode, file(readsFile) from Reads_ch

    output:
    tuple fileCode, file("${fileCode}.fasta") into Kmer_ch

    script:
    """
    unpigz -cp${task.cpus} $readsFile | paste - - - - | cut -f 1,2 | sed 's/^@/>/' | tr "\\t" "\\n" > ${fileCode}.fasta
    """
}

process Kmer {
    tag "Processing $fileCode reads files using kmer-ssr"
    maxForks params.threads
    cpus params.threads_kmer

    input:
    set fileCode, file(readsFile) from Kmer_ch

    output:
    tuple fileCode, file("${fileCode}.tsv") into ComputedReads_ch

    script:
    """
    kmer-ssr -d -t ${task.cpus} -p ${params.kmerSSR.periodMin}-${params.kmerSSR.periodMax} -n ${params.kmerSSR.ssrSizeTreshold} -r ${params.kmerSSR.repeatMin} -l ${params.kmerSSR.readLengthMin} -i ${fileCode}.fasta -o ${fileCode}.tsv
    """
}

When the pipeline is broken, I try to run again with nextflow run -resume and the problem is that all sequences from SRA are downloaded again ?? and the pipeline starts again from the beginning instead of resuming the job where it was interrupted. What is the problem, please ? Thanks.

$\endgroup$

0

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Browse other questions tagged or ask your own question.