--no-compute-checksum doesn't seem to be honored

[keiranmraine]

Expected Behavior

checksum should not be calculated when cwltool --no-compute-checksum ... is in use

Actual Behavior

I'm seeing the checksum's being written to stdout.

Executing with

cwltool --no-compute-checksum --enable-dev --non-strict\
 --outdir /home/ubuntu/datastore//launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/\
 --tmpdir-prefix /home/ubuntu/datastore//launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/tmp/\
 --tmp-outdir-prefix /home/ubuntu/datastore//launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/working/\
 /home/ubuntu/Dockstore_bam.cwl\
 /home/ubuntu/datastore//launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/workflow_params.json

Output

{
    "out_bam": {
        "checksum": "sha1$e9e4c479937e797baf0f570b71bff0fd6de71138", 
        "basename": "test.bam", 
        "location": "file:///home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam", 
        "secondaryFiles": [
            {
                "checksum": "sha1$1338447f52c9973e9bcb7ea79a2c4edffd3d815a", 
                "basename": "test.bam.bai", 
                "location": "file:///home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.bai", 
                "path": "/home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.bai", 
                "class": "File", 
                "size": 951528
            }, 
            {
                "checksum": "sha1$1a70259925f883e4a4856b225339e943c535996d", 
                "basename": "test.bam.bas", 
                "location": "file:///home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.bas", 
                "path": "/home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.bas", 
                "class": "File", 
                "size": 660
            }, 
            {
                "checksum": "sha1$12ad46945f5daae7afe44f59d84b6d3a3334ca40", 
                "basename": "test.bam.md5", 
                "location": "file:///home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.md5", 
                "path": "/home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.md5", 
                "class": "File", 
                "size": 32
            }, 
            {
                "checksum": "sha1$6414f4853c802bc08ac9e89acd33325b6846ece9", 
                "basename": "test.bam.met", 
                "location": "file:///home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.met", 
                "path": "/home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.met", 
                "class": "File", 
                "size": 1471
            }, 
            {
                "checksum": "sha1$02cd48fc01ed7aa23b42e285a84bc36acf923eb3", 
                "basename": "test.bam.maptime", 
                "location": "file:///home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.maptime", 
                "path": "/home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam.maptime", 
                "class": "File", 
                "size": 394
            }
        ], 
        "path": "/home/ubuntu/datastore/launcher-da4b0f53-f4bd-41b7-95d3-7de71a519054/outputs/test.bam", 
        "class": "File", 
        "size": 6600410
    }
}

Your Environment

/usr/local/bin/cwltool 1.0.20170828135420

[keiranmraine]

Just confirmed this occurs on configs without secondaryFiles directives.