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    Matt

    @Matt

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    Posts made by Matt

    • RE: How to...

      How to re-use a file channel and indeterminate number of times (eg combining with a channle with an unknkown number of elements in NextFlow DSL1:

      process collectGVCF {
        publishDir "${params.combined_1_vcf}", mode: 'copy'
      
        output:
          set val(pair_id), val(round), file("${pair_id}_raw_variants_${round}.vcf.gz") into collected_vcf
      }
      
      // Later after splitting:
      sample_files
        .map { it -> it.getBaseName() }
        .combine(Channel.fromPath("${params.combined_1_vcf}/*_raw_variants_1.vcf.gz"))
        .set { reuse_pairs }
      
      posted in Matt
      Matt
    • RE: How to...

      How to conditionally choose from two channels in NextFlow:

      grouped_interval_vcf_ch=(params.splitIntervalOverlapLength && params.splitIntervalOverlapLength.toInteger() > 0
      	? trimmed_vcf_ch
      	: interval_vcfs_3
      )
      
      posted in Matt
      Matt
    • RE: How to...

      How to collect all files related by prefix in NextFlow:

      Example input channel:

      interval_bams_ch:
      [ file('73-50_L001_raw_variants_1.bam') ]
      [ file('73-50_L001_raw_variants_2.bam') ]
      [ file('73-50_L002_raw_variants_1.bam') ]
      [ file('73-50_L002_raw_variants_2.bam') ]

      Process code:

      bam_name_parts_ch = interval_bams_ch.map { file ->
          def name = file.baseName.replaceFirst(/_raw_variants_.*/, '')
          tuple(name, file)
      }.groupTuple()
      

      Example output:

      [ '73-50_L001', [file('73-50_L001_raw_variants_1.bam'), file('73-50_L001_raw_variants_2.bam')] ]
      [ '73-50_L002', [file('73-50_L002_raw_variants_1.bam'), file('73-50_L002_raw_variants_2.bam')] ]

      posted in Matt
      Matt
    • RE: How to...

      How to collect all files from one channel and associate/combine them with elements of another channel in NextFlow:

      Example Input channels:

      bam_for_collect_ch2:
      [ file('73-50_L002.bam') ]
      [ file('73-50_L001.bam') ]

      interval_vcfs_3:
      [ file('73-50_L001_raw_variants_1.vcf.gz') ]
      [ file('73-50_L001_raw_variants_2.vcf.gz') ]
      [ file('73-50_L002_raw_variants_1.vcf.gz') ]
      [ file('73-50_L002_raw_variants_2.vcf.gz') ]

      Process code:

      input:
      set val(pair_id), val(all_vcf) from bam_for_collect_ch2.map({ file -> file.baseName }).combine(interval_vcfs_3.collect().map({ file -> file.baseName }).toList())
      

      Example output:

      [ '73-50_L002', ['73-50_L002_raw_variants_1.vcf.gz', '73-50_L002_raw_variants_2.vcf.gz'] ]
      [ '73-50_L001', ['73-50_L001_raw_variants_1.vcf.gz', '73-50_L001_raw_variants_2.vcf.gz'] ]

      posted in Matt
      Matt
    • RE: Links

      Turing machine simulator

      posted in Matt
      Matt
    • RE: How to...

      How to get rid of "WARNING : No mitochondrion chromosome found" in SnpEff:

      Prefix the contig name with MT.

      posted in Matt
      Matt
    • RE: Links

      KASP assay design

      posted in Matt
      Matt
    • RE: How to...

      How to clone a public GitHub repository with VS Code and push it to a private GitHub repository.

      • Make sure Git is installed
      • Open VS Code and use the source control icon on the far left to clone a git repository to a local folder
        503ebed1-4ee0-4739-9e75-2888814b4ddb-image.png

      Open a terminal in VS Code (View>terminal)

      PS C:\Users\github> cd sarek
      PS C:\Users\github\sarek> git remote remove origin
      PS C:\Users\github\sarek> git remote add origin https://github.com/ink-blot/sarek.git
      PS C:\Users\github\sarek> git branch
      * master
      PS C:\Users\github\sarek> git push -u origin master
      

      If it doesn't promptly start pushing, an authorisation screen should (eventually) appear (it may take a few minutes).

      92b031e2-3d77-414f-a4f3-1221b9f8afb6-image.png

      The token method is preferred:

      • Go to your GitHub account settings: GitHub Token Settings.
      • Click Generate new token (classic).
      • Select the scopes you need (e.g., repo for private repositories).
      • Generate the token and copy it (you won’t be able to see it again later).
      • In the GitHub sign-in window, switch to the Token tab.
      • Paste the generated token into the input field and confirm.

      Optional steps if you want to fetch updates from the original nf-core/sarek repository in the future, add it as an upstream remote:

      
      PS C:\Users\github\sarek> git remote add upstream https://github.com/nf-core/sarek.git
      PS C:\Users\github\sarek> git fetch upstream
      PS C:\Users\github\sarek> git merge upstream/main
      
      
      posted in Matt
      Matt
    • RE: Flower Photos

      cinema_DSC06111.JPG

      posted in Matt
      Matt