CreateFileRequirement: input_dir and work_dir are the same

[portah]

Gitter log:

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

[tetron]

This should be fixed in d1b787d, can you test?

[portah]

I've used workflows tests for samtools-faidx

• If file in the current working directory, then index created and everything fine
• if file in different directory lets say test-files/dm3_chr4.fa the the symlink is created but not accessible within docker

/usr/local/bin/cwl-runner 1.0.20151212191646
[job 4456508240] /Users/porter/Work/scidap/workflows/test$ docker run -i --volume=/Users/porter/Work/scidap/workflows/test/test-files/dm3_chr4.fa:/tmp/job958226343_test-files/dm3_chr4.fa:ro --volume=/Users/porter/Work/scidap/workflows/test:/tmp/job_output:rw --volume=/var/folders/hx/3qsmpl9s50zdmn49jb03l_tw0000gn/T/tmpj4hWug:/tmp/job_tmp:rw --workdir=/tmp/job_output --read-only=true --user=1000 --rm --env=TMPDIR=/tmp/job_tmp --env=PATH=/usr/local/bin/:/usr/bin:/bin scidap/samtools:v1.2-242-4d56437 samtools faidx dm3_chr4.fa
[fai_build] fail to open the FASTA file dm3_chr4.fa

• and if symlink already exists in the current working directory I have file exists error