PrivilegedUser's Group-1

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 }

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
)

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')] ]

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'] ]

Turing machine simulator

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

Prefix the contig name with MT.

KASP assay design

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
  

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).

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