All the elements in the group tuple do not get run in the presence of certain process

[shubavarshini]

Hi there,
I'm building a pipeline to quantify metagenomic data. I have the following processes defined: bbduk --> prefilterIndex_nodecoy --> prefiltering --> filtered_pangenomes --> salmonIndex_nodecoy --> salmon_quantification --> combing_salmon_files. I'm still testing hence certain part of the pipeline is yet to be tested and I use 6 mock samples for the same.

Coming to my issue: When I do not run the process "prefilterIndex_nodecoy" and provide the necessary index files, all the 6 samples get quantified in the process "salmon_quantification". But in the presence of the process "prefilterIndex_nodecoy", only one sample (I'm guessing which is the last to be processed by bbduk) is alone quantified in the process "salmon_quantification". There are no errors in the log file. And when I view the channel, it has all the 6 samples store as a tuple. I'm very confused as I cannot see the obvious mistake. Any help would be good.
Following are the details about my runs and scripts:

1. nextflow version 21.04.0.5552
2. main nextflow script: https://github.com/shubavarshini/microbiome/blob/master/microbiomeQuantification.nf
3. configuration file and conda environments: https://github.com/shubavarshini/microbiome

Please let me know if you cannot access the files.