# Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: Apache-2.0 - job: dir-job.yml output: "outlist": { "size": 20, "location": "output.txt", "class": "File", "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592" } tool: keep-dir-test-input.cwl doc: Test directory in keep - job: dir-job2.yml output: "outlist": { "size": 20, "location": "output.txt", "class": "File", "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592" } tool: keep-dir-test-input.cwl doc: Test directory in keep - job: null output: "outlist": { "size": 20, "location": "output.txt", "class": "File", "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592" } tool: keep-dir-test-input2.cwl doc: Test default directory in keep - job: null output: "outlist": { "size": 20, "location": "output.txt", "class": "File", "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592" } tool: keep-dir-test-input3.cwl doc: Test default directory in keep - job: octo.yml output: {} tool: cat.cwl doc: Test hashes in filenames - job: listing-job.yml output: { "out": { "class": "File", "location": "output.txt", "size": 5, "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1" } } tool: wf/listing_shallow.cwl doc: test shallow directory listing - job: listing-job.yml output: { "out": { "class": "File", "location": "output.txt", "size": 5, "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1" } } tool: wf/listing_none.cwl doc: test no directory listing - job: listing-job.yml output: { "out": { "class": "File", "location": "output.txt", "size": 5, "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1" } } tool: wf/listing_deep.cwl doc: test deep directory listing - job: null output: {} tool: noreuse.cwl doc: "Test arv:ReuseRequirement" - job: 12213-keepref-job.yml output: { "out": [ { "checksum": "sha1$1c78028c0d69163391eef89316b44a57bde3fead", "location": "sample1_S01_R1_001.fastq.txt", "class": "File", "size": 32 }, { "checksum": "sha1$5f3b4df1b0f7fdced751fc6079778600ad9fdb45", "location": "sample2_S01_R1_001.fastq.txt", "class": "File", "size": 32 } ] } tool: 12213-keepref-wf.cwl doc: "Test manipulating keep references with expression tools" - job: null output: out: null tool: 12418-glob-empty-collection.cwl doc: "Test glob output on empty collection" - job: null output: "out": { "location": "hello.out", "class": "File", "checksum": "sha1$ec5d3976351abab45a483a49ce714a8430cb203a", "size": 24 } tool: 13976-keepref-wf.cwl doc: "Test issue 13976" - job: null output: out: out tool: wf/runin-wf.cwl doc: "RunInSingleContainer cwl.input.json needs to be consistent with pathmapper manipulations" - job: secondary/wf-job.yml output: {} tool: secondary/wf.cwl doc: "RunInSingleContainer applies secondaryFile discovery & manipulation before generating cwl.input.yml" - job: null output: out: out tool: wf/runin-with-ttl-wf.cwl doc: "RunInSingleContainer respects outputTTL" - job: secret_test_job.yml output: { "out": { "class": "File", "location": "hashed_example.txt", "size": 47, "checksum": "sha1$f45341c7f03b4dd10646c402908d1aea0d580f5d" } } tool: wf/secret_wf.cwl doc: "Test secret input parameters" tags: [ secrets ] - job: null output: out: null tool: wf/runin-reqs-wf.cwl doc: "RunInSingleContainer handles dynamic resource requests on step" - job: null output: out: null tool: wf/runin-reqs-wf2.cwl doc: "RunInSingleContainer handles dynamic resource requests on embedded subworkflow" - job: null output: out: null tool: wf/runin-reqs-wf3.cwl should_fail: true doc: "RunInSingleContainer disallows dynamic resource request on subworkflow steps" - job: null output: out: null tool: wf/runin-reqs-wf4.cwl doc: "RunInSingleContainer discovers static resource request in subworkflow steps" - job: null output: out: null tool: wf/runin-reqs-wf5.cwl doc: "RunInSingleContainer has minimum 128 MiB RAM" - job: secondaryFiles/inp3.yml output: {} tool: secondaryFiles/example1.cwl doc: Discover secondaryFiles at runtime if they are in keep - job: null output: {} tool: secondaryFiles/example3.cwl doc: Discover secondaryFiles on default values - job: null output: out: null tool: wf-defaults/wf1.cwl doc: "Can have separate default parameters including directory and file inside same directory" - job: null output: out: null tool: wf-defaults/wf2.cwl doc: "Can have a parameter default value that is a directory literal with a file literal" - job: null output: out: null tool: wf-defaults/wf3.cwl doc: "Do not accept a directory literal without a basename" should_fail: true - job: null output: out: null tool: wf-defaults/wf4.cwl doc: default in embedded subworkflow missing 'id' field, v1.0 should_fail: true - job: null output: out: null tool: wf-defaults/wf8.cwl doc: default in embedded subworkflow missing 'id' field, v1.1 should_fail: false - job: null output: out: null tool: wf-defaults/wf5.cwl doc: default in embedded subworkflow - job: null output: out: null tool: wf-defaults/wf6.cwl doc: default in RunInSingleContainer step - job: null output: out: null tool: wf-defaults/wf7.cwl doc: workflow level default in RunInSingleContainer - job: 13931-size-job.yml output: "out": { "checksum": "sha1$5bf6e5357bd42a6b1d2a3a040e16a91490064d26", "location": "size.txt", "class": "File", "size": 3 } tool: 13931-size.cwl doc: Test that size is set for files in Keep - job: 15241-writable-dir-job.json output: { "results": { "basename": "keep:6dd5fa20622d5a7a23c9147d0927da2a+180", "class": "Directory", "listing": [ { "basename": "d7514270f356df848477718d58308cc4+94", "class": "Directory", "listing": [ { "basename": "a", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "a", "size": 0 }, { "basename": "blurg.txt", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "blurg.txt", "size": 0 }, { "basename": "c", "class": "Directory", "listing": [ { "basename": "d", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "d", "size": 0 } ], "location": "c" }, { "basename": "b", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "b", "size": 0 } ], "location": "d7514270f356df848477718d58308cc4+94" } ], "location": "keep:6dd5fa20622d5a7a23c9147d0927da2a+180" } } tool: 15241-writable-dir.cwl doc: Test for writable collections - job: badkeep.yml output: {} should_fail: true tool: 15295-bad-keep-ref.cwl doc: Test checking for invalid keepref - job: listing-job.yml output: { "out": { "class": "File", "location": "output.txt", "size": 5, "checksum": "sha1$724ba28f4a9a1b472057ff99511ed393a45552e1" } } tool: 16169-no-listing-hint.cwl doc: "Test cwltool:LoadListingRequirement propagation" - job: hello.yml output: "out": { "location": "hello.out", "class": "File", "checksum": "sha1$ec5d3976351abab45a483a49ce714a8430cb203a", "size": 24 } tool: 16377-missing-default.cwl doc: "Test issue 16377 - missing default fails even when it should be overridden by valid input" - job: hello.yml output: "out": "checksum": "sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15" "class": "File" "location": "foo.txt" "size": 4 tool: 17267-broken-schemas.cwl doc: "Test issue 17267 - inaccessible $schemas URL is not a fatal error" - job: null output: {} tool: wf/trick_defaults2.cwl doc: "Test issue 17462 - secondary file objects on file defaults are not resolved" - job: null output: { "stuff": { "location": "bar.txt", "basename": "bar.txt", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0 } } tool: 17521-dot-slash-glob.cwl doc: "Test issue 17521 - bug with leading './' capturing files in subdirectories" - job: null output: { "stuff": { "basename": "foo", "class": "Directory", "listing": [ { "basename": "bar.txt", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "foo/bar.txt", "size": 0 } ], "location": "foo" } } tool: 10380-trailing-slash-dir.cwl doc: "Test issue 10380 - bug with trailing slash when capturing an output directory" - job: null output: { "stuff": { "basename": "78f3957c41d044352303a3fa326dff1e+102", "class": "Directory", "listing": [ { "basename": "baz.txt", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "78f3957c41d044352303a3fa326dff1e+102/baz.txt", "size": 0 }, { "basename": "foo", "class": "Directory", "listing": [ { "basename": "bar.txt", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "class": "File", "location": "78f3957c41d044352303a3fa326dff1e+102/foo/bar.txt", "size": 0 } ], "location": "78f3957c41d044352303a3fa326dff1e+102/foo" } ], "location": "78f3957c41d044352303a3fa326dff1e+102" } } tool: 17801-runtime-outdir.cwl doc: "Test issue 17801 - bug using $(runtime.outdir) to capture the output directory" - job: null output: "val": "keep:f225e6259bdd63bc7240599648dde9f1+97/hg19.fa" tool: 17858-pack-visit-crash.cwl doc: "Test issue 17858 - keep ref default inputs on ExpressionTool"