Closed tiborsimko closed 1 year ago
Current behaviour
Consider the reana-demo-helloworld demo example, but with hard-coded values:
reana-demo-helloworld
diff --git a/workflow/snakemake/Snakefile b/workflow/snakemake/Snakefile index e7344f2..fc8e3a9 100644 --- a/workflow/snakemake/Snakefile +++ b/workflow/snakemake/Snakefile @@ -19,10 +19,8 @@ rule all: rule helloworld: input: - helloworld=config["helloworld"], - inputfile=config["inputfile"], - params: - sleeptime=config["sleeptime"] + helloworld="code/helloworld.py", + inputfile="data/names.txt", output: "results/greetings.txt" container: @@ -31,4 +29,4 @@ rule helloworld: "python {input.helloworld} " "--inputfile {input.inputfile} " "--outputfile {output} " - "--sleeptime {params.sleeptime}" + "--sleeptime 0" diff --git a/workflow/snakemake/inputs.yaml b/workflow/snakemake/inputs.yaml index 0a507cc..20e9ff3 100644 --- a/workflow/snakemake/inputs.yaml +++ b/workflow/snakemake/inputs.yaml @@ -1,3 +1 @@ -sleeptime: 0 -helloworld: code/helloworld.py -inputfile: data/names.txt +foo: bar
If you run the workflow:
$ reana-dev run-example -c r-d-helloworld -w snakemake
then everything works.
However, not that inputs.yaml is not really necessary in this case. If I try to remove it:
inputs.yaml
diff --git a/reana-snakemake.yaml b/reana-snakemake.yaml index 49cb624..3531372 100644 --- a/reana-snakemake.yaml +++ b/reana-snakemake.yaml @@ -5,8 +5,6 @@ inputs: - data/names.txt directories: - workflow/snakemake - parameters: - input: workflow/snakemake/inputs.yaml workflow: type: snakemake file: workflow/snakemake/Snakefile
then things break and the workflow cannot be submitted:
$ reana-dev run-example -c r-d-helloworld -w snakemake ... [WARNING] Job stats: job count min threads max threads ---------- ------- ------------- ------------- all 1 1 1 helloworld 1 1 1 total 2 1 1 ==> ERROR: Cannot create workflow helloworld-snakemake-kubernetes: 'parameters'
Expected behaviour
If a workflow does not need parameters, then we should allow its submission.
It may be good to make the "parameters" property optional for those workflows that do not really require it.
Current behaviour
Consider the
reana-demo-helloworld
demo example, but with hard-coded values:If you run the workflow:
then everything works.
However, not that
inputs.yaml
is not really necessary in this case. If I try to remove it:then things break and the workflow cannot be submitted:
Expected behaviour
If a workflow does not need parameters, then we should allow its submission.
It may be good to make the "parameters" property optional for those workflows that do not really require it.