Some changes to review

[gavin-peng]

1, Added Pipefile for the packages, some version upgraded
2, Change in utils.py, this is trying to fix the issue when saw error:

Traceback (most recent call last):
  File "/.mounts/labs/gsi/modulator/sw/Ubuntu20.04/deep-tumour-3.0.3/src/DeepTumour.py", line 222, in <module>
    DeepTumour()
  File "/.mounts/labs/gsi/modulator/sw/Ubuntu20.04/deep-tumour-3.0.3/.venv/lib/python3.10/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/.mounts/labs/gsi/modulator/sw/Ubuntu20.04/deep-tumour-3.0.3/.venv/lib/python3.10/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/.mounts/labs/gsi/modulator/sw/Ubuntu20.04/deep-tumour-3.0.3/.venv/lib/python3.10/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/.mounts/labs/gsi/modulator/sw/Ubuntu20.04/deep-tumour-3.0.3/.venv/lib/python3.10/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/.mounts/labs/gsi/modulator/sw/Ubuntu20.04/deep-tumour-3.0.3/src/DeepTumour.py", line 173, in DeepTumour
    input = vcf2input(vcfFile, refGenome, hg38)
  File "/.mounts/labs/gsi/modulator/sw/Ubuntu20.04/deep-tumour-3.0.3/src/utils.py", line 265, in vcf2input
    mutations:pd.DataFrame = df2mut(df, sample_name, fasta)
  File "/.mounts/labs/gsi/modulator/sw/Ubuntu20.04/deep-tumour-3.0.3/src/utils.py", line 203, in df2mut
    if (ref != ref_ctx[1]):
IndexError: string index out of range

The error came after we added step for filtering vcf calls, using bed file generated from filtering maf, and related to coordinates conversion:
https://github.com/oicr-gsi/deepTumourWorkflow/blob/gavin_updates/deepTumour.wdl#L121

[GFJHogue]

Just making a couple of tweaks to this in #7