Cannot execute the test run

[zhuweix]

Cheers,

I am trying to use the fibertools for m6a analysis. I make a fresh mamba environment according to the install.md.
I tested the installation by your test sample:

snakemake \ --profile profile/local \ --config \ env="fiberseq-smk" \ test=.test/ccs.bam \ ref=.test/ref.fa

However, I found such error message

Using profile profile/local for setting default command line arguments.
/gpfs/gsfs12/users/xuz5/github/fiberseq-smk/workflow/Snakefile:122: SyntaxWarning: invalid escape sequence '\d'

fiber table

Building DAG of jobs...
File path ' results/test/test.fiberseq.bam .pbi ' starts with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
File path ' results/test/test.fiberseq.bam .pbi ' ends with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
File path ' results/test/test.fiberseq.bam .pbi ' starts with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
File path ' results/test/test.fiberseq.bam .pbi ' ends with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
MissingInputException in rule merge in file /gpfs/gsfs12/users/xuz5/github/fiberseq-smk/workflow/rules/fiberseq-bam.smk, line 175:
Missing input files for rule merge:
output: results/test/test.fiberseq.bam, results/test/test.fiberseq.bam.bai
wildcards: sm=test
affected files:
temp/test/align. 1 -of- 1 .bam

I wonder if there is a typo for whitespace in the source code.

[DavYang]

I am also experiencing the same issue with the test case.

[mrvollger]

We have replaced this pipeline with ft, a binary that replaces this pipeline in a single command!

This note has been added to the readme, and our effort is going to be focused on this new tool.

sorry!