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Include all tools in initial --run parameter #39

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54 changes: 18 additions & 36 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -377,26 +377,8 @@ workflow NF_CANARY {
gpu

main:
def default_run_tools = [
"TEST_SUCCESS",
"TEST_CREATE_FILE",
"TEST_MV_FILE",
"TEST_CREATE_EMPTY_FILE",
"TEST_CREATE_FOLDER",
"TEST_INPUT",
"TEST_BIN_SCRIPT",
"TEST_STAGE_REMOTE",
"TEST_PASS_FILE",
"TEST_PASS_FOLDER",
"TEST_PUBLISH_FILE",
"TEST_PUBLISH_FOLDER",
"TEST_IGNORED_FAIL",
"TEST_GPU",
"TEST_MV_FOLDER_CONTENTS",
"TEST_VAL_INPUT"
]

def run = run_tools ? run_tools.tokenize(",")*.toUpperCase() : default_run_tools

def run = run_tools.tokenize(",")*.toUpperCase()
def skip = skip_tools.tokenize(",")*.toUpperCase()
Channel.fromList(run.findAll { it !in skip })
.flatten()
Expand Down Expand Up @@ -428,41 +410,41 @@ workflow NF_CANARY {
remote_file = params.remoteFile ? Channel.fromPath(params.remoteFile, glob:false) : Channel.empty()

// Run tests
TEST_SUCCESS( run_ch.TEST_SUCCESS )
TEST_CREATE_FILE( run_ch.TEST_CREATE_FILE )
TEST_BIN_SCRIPT( run_ch.TEST_BIN_SCRIPT )
TEST_CREATE_EMPTY_FILE( run_ch.TEST_CREATE_EMPTY_FILE )
TEST_CREATE_FILE( run_ch.TEST_CREATE_FILE )
TEST_CREATE_FOLDER( run_ch.TEST_CREATE_FOLDER )
TEST_GPU( run_ch.TEST_GPU, "dummy" )
TEST_IGNORED_FAIL( run_ch.TEST_IGNORED_FAIL )
TEST_INPUT( run_ch.TEST_INPUT, test_file )
TEST_BIN_SCRIPT( run_ch.TEST_BIN_SCRIPT )
TEST_STAGE_REMOTE( run_ch.TEST_STAGE_REMOTE, remote_file )
TEST_MV_FILE( run_ch.TEST_MV_FILE )
TEST_MV_FOLDER_CONTENTS(run_ch.TEST_MV_FOLDER_CONTENTS )
TEST_PASS_FILE( run_ch.TEST_PASS_FILE, TEST_CREATE_FILE.out.outfile )
TEST_PASS_FOLDER( run_ch.TEST_PASS_FOLDER, TEST_CREATE_FOLDER.out.outfolder )
TEST_PUBLISH_FILE( run_ch.TEST_PUBLISH_FILE )
TEST_PUBLISH_FOLDER( run_ch.TEST_PUBLISH_FOLDER )
TEST_IGNORED_FAIL( run_ch.TEST_IGNORED_FAIL )
TEST_MV_FILE( run_ch.TEST_MV_FILE )
TEST_MV_FOLDER_CONTENTS(run_ch.TEST_MV_FOLDER_CONTENTS )
TEST_STAGE_REMOTE( run_ch.TEST_STAGE_REMOTE, remote_file )
TEST_SUCCESS( run_ch.TEST_SUCCESS )
TEST_VAL_INPUT( run_ch.TEST_VAL_INPUT, "Hello World" )
TEST_GPU( run_ch.TEST_GPU, "dummy" )

// POC of emitting the channel
Channel.empty()
.mix(
TEST_SUCCESS.out,
TEST_CREATE_FILE.out,
TEST_BIN_SCRIPT.out,
TEST_CREATE_EMPTY_FILE.out,
TEST_CREATE_FILE.out,
TEST_CREATE_FOLDER.out,
TEST_GPU.out,
TEST_IGNORED_FAIL.out,
TEST_INPUT.out,
TEST_BIN_SCRIPT.out,
TEST_STAGE_REMOTE.out,
TEST_MV_FILE.out,
TEST_MV_FOLDER_CONTENTS.out,
TEST_PASS_FILE.out,
TEST_PASS_FOLDER.out,
TEST_PUBLISH_FILE.out,
TEST_PUBLISH_FOLDER.out,
TEST_IGNORED_FAIL.out,
TEST_MV_FILE.out,
TEST_MV_FOLDER_CONTENTS.out,
TEST_GPU.out
TEST_STAGE_REMOTE.out,
TEST_SUCCESS.out
)
.set { ch_out }

Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
params {
skip = ''
gpu = false
run = ''
run = "TEST_BIN_SCRIPT,TEST_CREATE_EMPTY_FILE,TEST_CREATE_FILE,TEST_CREATE_FOLDER,TEST_GPU,TEST_IGNORED_FAIL,TEST_INPUT,TEST_MV_FILE,TEST_MV_FOLDER_CONTENTS,TEST_PASS_FILE,TEST_PASS_FOLDER,TEST_PUBLISH_FILE,TEST_PUBLISH_FOLDER,TEST_STAGE_REMOTE,TEST_SUCCESS,TEST_VAL_INPUT"
outdir = null
remoteFile = null
container = "quay.io/biocontainers/ubuntu:24.04"
Expand Down
3 changes: 2 additions & 1 deletion nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@
"run": {
"type": "string",
"description": "Selectively run tests as comma delimited values",
"help_text": "Tests to run as comma delimited values. E.g. --skip TEST_SUCCESS,TEST_INPUT. Case insensitive. Note this excludes all other tests."
"help_text": "Tests to run, specified as comma-delimited values (e.g., --skip TEST_SUCCESS,TEST_INPUT). Case-insensitive. By default, all tests are included, but you can override this to selectively include specific tests.",
"default": "TEST_BIN_SCRIPT,TEST_CREATE_EMPTY_FILE,TEST_CREATE_FILE,TEST_CREATE_FOLDER,TEST_GPU,TEST_IGNORED_FAIL,TEST_INPUT,TEST_MV_FILE,TEST_MV_FOLDER_CONTENTS,TEST_PASS_FILE,TEST_PASS_FOLDER,TEST_PUBLISH_FILE,TEST_PUBLISH_FOLDER,TEST_STAGE_REMOTE,TEST_SUCCESS,TEST_VAL_INPUT"
},
"skip": {
"type": "string",
Expand Down