restore an option to do per-lane stats for QC

[golobor]

No description provided.

[sergpolly]

i.e. in other words go from this:

process merge_chunks_into_runs {
    tag "library:${library} run:${run}"
    storeDir getIntermediateDir('pairsam_run')
 
    input:
    set val(library), val(run), file(pairsam_chunks) from LIB_RUN_GROUP_PAIRSAMS
     
    output:
    set library, run, "${library}.${run}.pairsam.${suffix}" into LIB_RUN_PAIRSAMS
 
    script:
    // can we replace this part with just the "else" branch, so that pairsamtools merge will take care of it?
    if( isSingleFile(pairsam_chunks) )
        """
        ln -s \"\$(readlink -f ${pairsam_chunks})\" ${library}.${run}.pairsam.${suffix}
        """
    else
        """
        mkdir ./tmp4sort
        pairsamtools merge ${pairsam_chunks} --nproc ${task.cpus} -o ${library}.${run}.pairsam.${suffix} --tmpdir ./tmp4sort
        rm -rf ./tmp4sort
        """

to something like this:

process merge_chunks_into_runs {
    tag "library:${library} run:${run}"
    storeDir getIntermediateDir('pairsam_run')
    publishDir path:'.', mode:"copy", saveAs: {
      if( it.endsWith('.stats' ))
        return getOutDir("stats_lane") +"/${library}${run}.stats"
    }

    input:
    set val(library), val(run), file(pairsam_chunks) from LIB_RUN_GROUP_PAIRSAMS
     
    output:
    set library, run, "${library}.${run}.pairsam.${suffix}" into LIB_RUN_PAIRSAMS
 
    script:

    optional_stats_cmd = ( params.get('lane_stats','false').toBoolean() ? 
        "pairsamtools stats -o ${library}.${run}.stats ${library}.${run}.pairsam.${suffix}" : "" )

    // can we replace this part with just the "else" branch, so that pairsamtools merge will take care of it?
    if( isSingleFile(pairsam_chunks) )
        """
        ln -s \"\$(readlink -f ${pairsam_chunks})\" ${library}.${run}.pairsam.${suffix}
        ${optional_stats_cmd}
        """
    else
        """
        mkdir ./tmp4sort
        pairsamtools merge ${pairsam_chunks} --nproc ${task.cpus} -o ${library}.${run}.pairsam.${suffix} --tmpdir ./tmp4sort
        ${optional_stats_cmd}
        rm -rf ./tmp4sort
        """

something like that

just do it more carefully

[golobor]

yes, this seems legit to me. I wouldn't even know how to make it more careful than this 👍

[golobor]

with one exception - what does this line do?
optional_stats_cmd = params['map'].get('drop_sam','false').toBoolean()

[sergpolly]

copi pasta

[sergpolly]

i've edited the comment to remove it.
I'll test this whenever i can ...

[mimakaev]

Hi guys. I just realized that not even per-lane stats are missing, but per-library stats as well. Is that intentional? I find it very limiting not to have stats for replicates.

EDIT: found them in the pairs folder. Maybe we should put them in a separate folder? or is it too difficult?

[Phlya]

Is there really any reason why the code from above is not merged? Should this be done together with the stats format change? open2c/pairtools#79