nextflow-io/nextflow

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Alaa Badredine

@AlaaBadredine_twitter

I mean it is cached I believe but somehow he's not able to recognize the index

and that's the script block inside the copy:

    script:
        """
        cp ${nfPath} ${toScripts}
        cp ${params.sampleSheet} ${toRaw}/SampleSheet.csv
        cp -r \$(dirname "${workflow.scriptFile}")/bin ${toScripts}
        echo ${params.userName} > ${toLogs}/user.txt

        echo ${capture} > capture.txt
        echo ${dbsnp} > dbsnp.txt
        echo ${knownSites1} >> dbsnp.txt
        echo ${knownSites2} >> dbsnp.txt

        cp --verbose -rf ${fromNAS}/* ${toRaw} 2> copy.log

        #rsync -a ${fromNAS}/ ${toRaw} --log-file=rsync.log
        #rsync --version > rsync_version.txt

        $lbzip2 -n 10 --best copy.log
        #$lbzip2 -n 10 --best rsync.log

        touch copyProcess.ok
        """

Stijn van Dongen

@micans

Alright, it's hard to tell from here. I'd try to make a small toy example if that's possible.

Alaa Badredine

@AlaaBadredine_twitter

I shall do that

thanks

Stijn van Dongen

@micans

yw, good luck!

Stijn van Dongen

@micans

@pditommaso as an alternative to this pattern: http://nextflow-io.github.io/patterns/index.html#_problem_19
I've made https://github.com/micans/nextflow-idioms/blob/master/ab-abc-until.nf
It uses

ch_skipB.until {  params.doB }.set { ch_AC }
ch_doB.until { !params.doB }.set { ch_AB }

Instead of

(ch_AC, ch_AB) = ( params.doB ? [Channel.empty(), ch_doB] : [ch_skipB, Channel.empty()] )

This made me wonder; first if there is a drawback to using until like this, and second, the example uses into { ch_doB; ch_skipB } just before. I am envisioning into syntax extended like this:

into { .until{  params.doB }.set{ ch_AC }; 
       .until{ !params.doB }.set{ ch_AB }
     }

I'm not sure it's possible or that useful, but wanted to document the thought. []

Riccardo Giannico

@giannicorik_twitter

@AlaaBadredine_twitter do you see this file to be created ${toRaw}/SampleSheet.csv? I'm wandering if you have write permissions under ${toRaw} .
Does the .nextflow.log file report any error? Does it report if the process you need has been "submitted" or "chached" ?

Alaa Badredine

@AlaaBadredine_twitter

@giannicorik_twitter yes I do, after all, the system we have here is only under root, so we don't have issues with writing/reading permissions

bit of weird tbh but that's how it is

Michael Adkins

@madkinsz

Hi! I have a question about parsing variables from the input channel made fromPath. I'm interested in parsing project names from a path doing operations on entire projects. Here's kind of a pseudocode pipeline: https://hastebin.com/raw/tutifepuxa

I can't really find any clear documentation about how to parse variables from paths

danchubb

@danchubb

Hi, I'm enjoying getting the hang of nextflow but I've hit a brick wall with what is hopefully a simple problem. When parsing a csv file using splitCsv() how do you access columns where the header has spaces? e.g. if the col is filename then it is ${row.filename} what if it is "file name" ? backticks? quotes? Thanks a lot - Dan

Stijn van Dongen

@micans

@danchubb I had a quick try, this seems to work:

#!/usr/bin/env nextflow
Channel
    .from( 'alpha,beta,gam ma\n10,20,30\n70,80,90' )
    .splitCsv(header: true)
    .subscribe { row ->
       println "${row.alpha} - ${row.beta} - ${row.'gam ma'}"
    }

(edited to show it's easy to test a small snippet -- this was taken from the splitCsv documentation)

danchubb

@danchubb

great, thanks a lot for the help.

Michael Adkins

@madkinsz

Does nextflow attempt to ignore duplicating input files as output files? e.g. I'm getting an error: Missing output file(s) *.fastq expected by process merge_nextseq_lanes when calling a script that renames files in place. There are many .fastq files in the working directory but it cannot find any?

Paolo Di Tommaso

@pditommaso

input file names are not captured by globs

Michael Adkins

@madkinsz

Is there a way to make them captured?

Or is calling a script to combine/rename some of the files bad practice? I want to take a collection, rename a small subset or combine some, then pass all the resulting files as a new channel

Paolo Di Tommaso

@pditommaso

not a good idea, a task should produce its own outputs

Michael Adkins

@madkinsz

Okay, I don't understand how preprocessing tasks are supposed to work then. I have a tool that needs to operate on all of the fastq files but some of the fastqs require preprocessing first.

Paolo Di Tommaso

@pditommaso

you can have the pre-proc task getting some of the fastqs, and another task getting all fastqs + out of the pre-proc

makes sense?

Michael Adkins

@madkinsz

That does make sense but I don't know how to exclude the ones that would be preprocessed from the all fastqs.

Since preprocessing requires all the fastqs to be collected so that some can be merged

Paolo Di Tommaso

@pditommaso

glob pattern? csv file? you should have a criteria to express that

Michael Adkins

@madkinsz

You're right. That should be reasonable, I'll look into that. Thank you.

Paolo Di Tommaso

@pditommaso

@micans the alternative may work (haven't tried), the second proposal it looks to much creative ..

Michael Adkins

@madkinsz

Can you use the channel factory / builder in the input/output parts of a process?

The connection between those two syntactic forms is kind of unclear

Stijn van Dongen

@micans

@pditommaso the alternative works ... (pretty sure, tested it). It's not that creative ... it unleashes huge possibilities :grin: ... I found the need to introduce extra channel names a little bit annoying ... so I was thinking about ways to get an implicit channel into into.

Paolo Di Tommaso

@pditommaso

you can create as many Channel.fromPath('foo*.fastq') as you need

I found the need to introduce extra channel names a little bit annoying

I understand, but dsl-2 won't require anymore to create channel dups

Michael Adkins

@madkinsz

@pditommaso but how do you use that within a process rather than at the head of a .nf file?

Stijn van Dongen

@micans

Cool @pditommaso I'll check it out. I think these extra names may be because of the a(b)c optional b process rather than into duplication, but will check for sure.

Paolo Di Tommaso

@pditommaso

ch1 = Channel.fromPath('*.fasta')
ch2 = Channel.fromPath('*.fasta')

process foo {
  input: 
  file x from ch1
  .. 
}

process bar {
  input: 
  file x from ch2
  .. 
}

@micans check it out! I need your feedback to move it on :D

and now :wave: :smile:

Stijn van Dongen

@micans

@madkinsz We link our fastq files in from a process; it gives a lot of control so you can do whatever you want. In our case the starting point is a sample file with IDs so we have explicit control. We then expect to find the fastq files in a directory. e.g. https://github.com/cellgeni/rnaseq/blob/master/main.nf#L269-L292

:wave: @pditommaso ah I thought there were lots of heavy users providing feedback already! I have a shortage of pipelines to do much abstraction. Anyway, will look nevertheless!

Michael Adkins

@madkinsz

I like what you have @micans. We expect to run this process on all the fastqs in a directory. My problem is this:

Oh geez -- edited to remove unformatted code

Sorry used to markdown.

Stijn van Dongen

@micans

(sorry have to run for dinner, will check later!)

Michael Adkins

@madkinsz

fastq_gz = Channel.fromPath('/cb/boostershot-basic/Data/Intensities/BaseCalls/CBTEST_Project_0091/*.fastq.gz')


process unzip_fastq {
  tag '$fastq_gz'

  input:
    file fastq_gz from fastq_gz

  output:
    file '*.fastq' into fastq_files

  script:
    """
    gunzip -df $fastq_gz
    """
}

Then I want to merge the lanes using a channel such as

fastq_pairs = Channel
    .fromFilePairs('/cb/boostershot-basic/Data/Intensities/BaseCalls/CBTEST_Project_0091/*_L00[1-4]_R[1-2]_001.fastq'), size: -1)

but I don't know how to make that channel read from the fastq_files channel

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