CreateFileRequirement: input_dir and work_dir are the same

Gitter log:

[samtools-faidx.cwl](https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-faidx.cwl)

@portah 12:26
But this solution will only work if out_dir different from input_dir
So as part of workflow it going to work, as stand_alone and being run in current dir will generate an error about file exist
Is there a way to rename a file after execution

@portah 12:37

```
[job 4415558160] /Users/porter/Work/scidap/workflows/tools$ docker run -i --volume=/Users/porter/Work/scidap/workflows/tools/./test-files/mm10.fa:/tmp/job877968402_test-files/mm10.fa:ro --volume=/Users/porter/Work/scidap/workflows/tools:/tmp/job_output:rw --volume=/var/folders/hx/3qsmpl9s50zdmn49jb03l_tw0000gn/T/tmpF_Wh4u:/tmp/job_tmp:rw --workdir=/tmp/job_output --user=1000 --rm --env=TMPDIR=/tmp/job_tmp --env=PATH=/usr/local/bin/:/usr/bin:/bin scidap/samtools:v1.2-216-gdffc67f samtools faidx mm10.fa
Final process status is success
{
"index_result": {
"path": "/Users/porter/Work/scidap/workflows/tools/mm10.fa.fai",
"size": 689,
"class": "File",
"checksum": "sha1$e7fef44bbe095319668b0c5a903d5b8ffa793080"
}
}%
```

But to run it standalone original input file has to be in separate directory
so I've run it `./samtools-faidx.cwl --input=./test-files/mm10.fa`

@tetron 13:34
@portah well, it could probabyl be smarter and not generate an error in that case
@portah when input_dir and work_dir are the same

@portah 13:41
Making pull request for samtools-faidx.cwl