Arvados

Container request mounts:

    "/keep/257d929aeba48f3a34ee3ad6cd6e1912+2101/55001703461433.chr1.bam": {
      "portable_data_hash": "257d929aeba48f3a34ee3ad6cd6e1912+2101",
      "kind": "collection",
      "path": "55001703461433.chr1.bam" 
    },
    "/keep/257d929aeba48f3a34ee3ad6cd6e1912+2101/55001703461433.chr1.bam.bai": {
      "portable_data_hash": "257d929aeba48f3a34ee3ad6cd6e1912+2101",
      "kind": "collection",
      "path": "55001703461433.chr1.bam.bai" 
    },

cwl.input.json:

  "samtools-index-bam": {
    "basename": "55001703461433.chr1.bam",
    "checksum": "sha1$d14040d6f85f4cb56ed31b5f964db085feca67fa",
    "class": "File",
    "location": "/keep/8079bc6e40be8ebbcd2f263966996725+2265/55001703461433.chr1.bam",
    "secondaryFiles": [
      {
        "basename": "55001703461433.chr1.bam.bai",
        "checksum": "sha1$0f47819ed3a744d52845ae2a306ce967c89fa90c",
        "class": "File",
        "location": "/keep/8079bc6e40be8ebbcd2f263966996725+2265/55001703461433.chr1.bam.bai",
        "size": 692656
      }
    ],
    "size": 3213913729
  }

Pathmapping copies the files to a new collection to improve container reuse, however when using RunInSingleContainer it happens after the cwl.input.json has been generated. Need to apply pathmapping to ensure that cwl.input.json and the actual input record are consistent.