Nextflow: Runs without error, produce few but not all output files into output channel

I was trying to develop a pipeline using nextflow and plink. My code runs without any error, but got only two output files instead of 22 (one for each chromosome). Here is part my code block, any help?

process step5 {
publishDir params.publish, mode: 'copy'
input:
val(hrc) from HRC_1000G_check_bim
val(hrc_site) from hrc_sites_file
tuple val(prefix), val(chr_name), path(bfiles) from step4_frq
output:
tuple val("$${prefix}"), val(chr_name), path("LOG-$${prefix}$${chr_name}.step4-HRC.txt") into step4_log tuple val("$${prefix}"), val(chr_name), path("Exclude-$${prefix}$${chr_name}.step4-HRC.txt") into step4_exclude
tuple val("$${prefix}"), val(chr_name), path("Chromosome-$${prefix}$${chr_name}.step4-HRC.txt") into step4_chromosome tuple val("$${prefix}"), val(chr_name), path("Position-$${prefix}$${chr_name}.step4-HRC.txt") into step4_position
tuple val("$${prefix}"), val(chr_name), path("Strand-Flip-$${prefix}$${chr_name}.step4-HRC.txt") into step4_strand tuple val("$${prefix}"), val(chr_name), path("Force-Allele1-$${prefix}$${chr_name}.step4-HRC.txt") into step4_allele
tuple val("$${prefix}"), val(chr_name), path("ID-$${prefix}$${chr_name}.step4-HRC.txt") into step4_id script: """ perl "$${hrc}" -b "$${prefix}$${chr_name}.step4.bim" -f "$${prefix}$${chr_name}.step4.frq" -r "${hrc_site}" -h """ }  The output files are: gsa-out/Chromosome-chr22.step4-HRC.txt gsa-out/Force-Allele1-chr3.step4-HRC.txt gsa-out/Position-chr22.step4-HRC.txt gsa-out/Chromosome-chr3.step4-HRC.txt gsa-out/ID-chr22.step4-HRC.txt gsa-out/Position-chr3.step4-HRC.txt gsa-out/Exclude-chr22.step4-HRC.txt gsa-out/ID-chr3.step4-HRC.txt gsa-out/Strand-Flip-chr22.step4-HRC.txt gsa-out/Exclude-chr3.step4-HRC.txt gsa-out/LOG-chr22.step4-HRC.txt gsa-out/Strand-Flip-chr3.step4-HRC.txt gsa-out/Force-Allele1-chr22.step4-HRC.txt gsa-out/LOG-chr3.step4-HRC.txt  I am not sure why I am getting only 2, instead of 22 output files. With similar output channel previously generated 22 output files in the same script. For eaxmple: process step1b { publishDir params.publish, mode: 'copy' input: tuple val(prefix), val(chr_name), path(bfiles) from step1a_out output: tuple val("$${prefix}"), val(chr_name), path("$${prefix}$${chr_name}.step1c.{bed,bim,fam}") into step1b_results path("$${prefix}$${chr_name}.step1c.log") into step1b_logs path("$${prefix}${chr_name}.step1b.snplist.txt") into step1b_snplist
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 ;}' "$${bfiles[1] }" | grep ambig > "$${prefix}$${chr_name}.step1b.snplist.txt" plink1.9 --bfile "$${prefix}$${chr_name}.step1b" --exclude "$${prefix}$${chr_name}.step1b.snplist.txt" --make-bed --out "$${prefix}${chr_name}.step1c" """ }  1 Answer I suspect your HRC_1000G_check_bim and hrc_sites_file channels are queue channels when they should be value channels. Please again see how multiple channels work. Also, third-party scripts, like your Perl script, would be better placed in a directory called bin/ at the root of your project repository. Nextflow adds this directory to your$PATH, so scripts in this directory will be automatically accessible in your pipeline without needing to localize them using a separate channel. This way also avoids having to specify an absolute path to invoke them. Just make sure your script is executable: chmod +x your_script.pl

hrc_sites = file( params.hrc_sites_file )

process step5 {

input:
tuple val(prefix), val(chr_name), path(bfiles) from step4_frq
path hrc_sites

"""
your_script.pl \\
-b "$${prefix}$${chr_name}.step4.bim" \\
-f "$${prefix}$${chr_name}.step4.frq" \\
-r "\${hrc_sites}" \\
-h
"""
}

• Thank you @Steve. I just avoided using channel for those two files. I need to use them from absolute path, because other users also use this pipeline. However, it works now. One thing, I am using slurm executor with a config file, so far no problem with this. But I want to run the script in background (similar to sbatch submit, after submitting the job I will logout and the job will continue to run). How could I do this? Mar 25 at 19:02
• One thing, After finishing the jobs, transferring files to publish directory taking too much time. There are only 264 files but it is taking hours to transfer. Any solution for this? Mar 25 at 20:59
• No worries at all @zillurrahman. It's generally better to avoid specifying absolute paths in your process scripts. Avoiding absolute paths will mean that your process tasks can be run in isolation from each other and that your users could run your workflow on platforms like AWS Batch where there is no shared filesystem. Mar 25 at 23:55
• I don't have experience with Slurm, but you should be able to submit a job non-interactively using sbatch like you said. If it's submitted non-interactively, you can logout and the job running your workflow will continue on. Mar 26 at 0:04
• You may also want to consider other publishing modes and parameterizing these, for example: mode: params.publish_mode. Consider also parameterizing the 'enabled' option so to let your users decide what outputs they want: enabled: params.publish_everything || params.publish_step5. HTH. Mar 26 at 0:28