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How could I filter outputs of a process in the input of the next process? Filtering works fine in channel, but if I try to filter outputs I got compilation error. I tried as follows:

Channel
.fromFilePairs("${params.dir}*.{bed,bim,fam}",size:3)
.set {data}
    process step1a {
    input:
    tuple val(sample_name), path(bfiles) from data
    output:
    tuple val("${prefix}"), path("${prefix}.{bed,bim,fam}") into (step1a_out,step1a_bim)
    script:
    """
    plink --bfile "${sample_name}" --chr 1-22 --out "${prefix}.step1b" --make-bed
    """
    }
    process step1b {
    input:
    tuple val(bim), path(bims) from step1a_bim.filter{bim, files -> name =~/*bim/}
    tuple val(sample_name), path(bfiles) from step1a_out
    output:
    path("${prefix}.step1b.snplist.txt")
    tuple val("${sample_name}"), path("${sample_name}.step1c.{bed,bim,fam}") into step1b_results
    script:
    """
    awk '{ if ((\\\$5=="T" && \\\$6=="A")||(\\\$5=="A" && \\\$6=="T")||(\\\$5=="C" && \\\$6=="G")||(\\\$5=="G" && \\\$6=="C")) print \\\$2, "ambig" ; else print \\\$2 ;}' "${prefix}.step1b.bim" | grep ambig > "${prefix}.step1b.snplist.txt"
    plink --bfile "${prefix}.step1b" --exclude "${prefix}.step1b.snplist.txt" --make-bed --out "${prefix}.step1c"
"""

It gives me

Compilation error
-cause: Unexpected input: '{'
process step1b {

Step1a gives me chr1.step1b.bed|bim|fam, chr2.step1b.bed|bim|fam.......chr22.step1b.bed|bim|fam (22 plink files) I need to access prefix of those outputs to run plink and other tools to generate chr1.step1c.bed|bim|fam ...chr22.step1c.bed|bim|fam (another 22 plink files). run awk to generate chr1.step1b.snplist.txt .... chr22.step1b.snplist.txt (22 txt files). Any help to filter the inputs so that I could use only *bim files from step1a_bim? Also how to select prefix of files in the input of processes that are from step1a_out to run plink? Does it make sense now?

Best Reagrds Zillur

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2
  • $\begingroup$ In case of a compilation error it is more useful if you post your actual code, properly formatted, and your error message. $\endgroup$
    – Pallie
    Mar 23 at 12:04
  • $\begingroup$ @Pallie, I edited my question above. Does it clarify my issues on outputs and inputs? $\endgroup$ Mar 23 at 13:07
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Instead of outputting all files and filtering for only bim, output only bims:

output:
tuple val("${prefix}"), path("${prefix}.{bed,bim,fam}") into (step1a_out,step1a_bim)

Do

output:
tuple val("${prefix}"), path("${prefix}.{bed,bim,fam}") into step1a_out
tuple val("${prefix}"), path("${prefix}.bim") into step1a_bim

So you can skip your complicated filter:

process step1b {
    input:
    tuple val(bim), path(bimfile) from step1a_bim
    output:
    path("${prefix}.step1b.snplist.txt")
tuple val("${sample_name}"), path("${sample_name}.step1c.{bed,bim,fam}") into 
step1b_results
    script:
    """
    awk '{ if ((\\\\\$5=="T" && \\\\\$6=="A")||(\\\\\$5=="A" && \\\\\$6=="T")||(\\\\\$5=="C" && \\\\\$6=="G")||(\\\\\$5=="G" && \\\\\$6=="C")) print \\\\\$2, "ambig" ; else print \\\\\$2 ;}' "$bimfile" | grep ambig > "${prefix}.step1b.snplist.txt"
    plink --bfile "${prefix}.step1b" --exclude "${prefix}.step1b.snplist.txt" --make-bed --out "${prefix}.step1c"

"""

```
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  • $\begingroup$ Thanks @Pallie . I tried your method. In that case, I got Process 'step1b' input file name collision -- There are multiple input files for each of the following file names: chr5.step1b.bim. Any suggestion? $\endgroup$ Mar 23 at 17:44
  • $\begingroup$ The step1a_bim is a subset of step1a_out which produce bed|bim|fam files. $\endgroup$ Mar 23 at 18:20
  • $\begingroup$ I could divide process step1b into two processes and could use step1a_out. But how could I use only *.bim files as input? Because step1a_out produce all *.bim, *.bed and *.fam files. For one process I need all three (bed|bim|fam) and for another I need only bim files. I am not sure how to subset the elements of a channel. $\endgroup$ Mar 23 at 19:01

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