How to...

Matt

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'] ]

Matt

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')] ]

Matt

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
)

Matt

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 }

Matt

How to apply for a Visa on Arrival for Indonesia online before you travel:

A Visa on Arrival (VOA) is available for passport holders in many countries including Australia. It costs US$35 (A$50) and is valid for 30 days. Follow the link below to apply.

https://evisa.imigrasi.go.id/

Matt

How to show fold changes in an excel spreadsheet when there are 0 values in the denominator. In the example below P30 is the numerator and P2 is the denominator. The logic is:

Both numerator and denominator = 0 → output 0.00
Denominator = 0, numerator ≠ 0 → output >{numerator} (2 decimals)
Numerator = 0, denominator ≠ 0 → output <{denominator} (2 decimals)
Otherwise → output normal division with 2 decimals.

=IF(AND(P30=0,P2=0),"0.00",
   IF(P2=0,">"&TEXT(P30,"0.00"),
      IF(P30=0,"<"&TEXT(P2,"0.00"),
         TEXT(P30/P2,"0.00"))))

Matt

How to search for a file on linux and suppress error messages and stop once the first instance is found:

find /home/files -xdev -type f -name 'P13.txt' -print -quit 2>/dev/null

Matt

How to withdraw money from a Commonwealth Bank ATM using your phone and the CommBank App.

On the ATM screen, select “Cardless Cash”
In the CommBank app go to 'Pay' > 'Cardless Withdrawal & Deposit ".
Using your phone, scan the QR code on the ATM screen.

Matt

How to enable root access in WinSCP:

Advanced>SFTP>SFTP server:

sudo /usr/lib/openssh/sftp-server

Matt

How to get comment balloons to reappear in the margins of a MS Word document:

Review>Show Comments>List

Then:

Review>Show Markup>Balloons>Show All Revisions Inline