tximport | summarize transcript-level estimates | Genomics library

I want to know if one can define a input rule that has dependencies on different wildcards.

To elaborate, I am running this Snakemake pipeline on different fastq files using qsub which submits each job to a different node:

1. fastqc on original fastq - no downstream dependency on other jobs
2. adapter/quality trimming to generate trimmed fastq
3. fastqc_after on trimmed fastq (output from step 2) and no downstream dependency
4. star-rsem pipeline on trimmed fastq (output from step 2 above)
5. rsem and tximport (output from step 4)
6. Run multiqc

MultiQC - https://multiqc.info/ - runs on the results folder which has results from fastqc, star, rsem, etc. However, because each job runs on a different node, sometimes Step 3 (fastqc and/or fastqc_after) is still running on the nodes while other steps finish running (Steps 2, 4 and 5) OR vice-versa.

Currently, I can create a MultiQc rule which waits on results from Steps 2, 4, 5 because they are linked to each other by input/output rules.

I have attached my pipeline as png to this post. Any suggestions would help.

What I need: I want to create a "collating" step where I want MultiQC to wait till all steps (from 1 to 5) finish. In other words, using my attached png as guide, I want to define multiple input rules for MultiQC that also wait on results from fastqc

Thanks in advance.

Note: Based on comments I received from 'colin' and 'bli' after my original post, I have shared the code for the different rules here.

Step 1 - fastqc