Summary lib function prints false as different to the schema when no default #971
Description
The NfcoreSchema lib function params_summary_map prints quite a lot of values for the summary when they do not vary from the schema.
- If a parameter in
nextflow.configis set tonullorfalseand the pipeline schema does not have a default parameter set - All memory and time units (string representation output is different to schema)
Example output from the nf-core/methylseq pipeline using -profile test:
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/methylseq v1.6
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Core Nextflow options
runName : awesome_minsky
containerEngine : docker
container : nfcore/methylseq:1.6
launchDir : /Users/ewels/GitHub/nf-core/methylseq/testing
workDir : /Users/ewels/GitHub/nf-core/methylseq/testing/work
projectDir : /Users/ewels/GitHub/nf-core/methylseq
userName : ewels
profile : test,docker
configFiles : /Users/ewels/GitHub/nf-core/methylseq/nextflow.config
Input/output options
input : null
single_end : true
email : false
Reference genome options
genome : false
fasta : https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa
fasta_index : https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai
bismark_index : false
bwa_meth_index : false
Bismark options
meth_cutoff : false
known_splices : false
minins : false
maxins : false
bismark_align_cpu_per_multicore: null
bismark_align_mem_per_multicore: null
Generic options
email_on_fail : false
max_multiqc_email_size : 25 MB
multiqc_config : false
Max job request options
max_cpus : 2
max_memory : 6 GB
max_time : 2d
Institutional config options
config_profile_name : Test profile
config_profile_description : Minimal test dataset to check pipeline function
config_profile_contact : false
config_profile_url : false
project : false
cluster_options : false
[Only displaying parameters that differ from pipeline default]
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I think that a lot of this is is because the schema default for strings is set to an empty string if it is not set:
tools/nf_core/pipeline-template/lib/NfcoreSchema.groovy
Lines 509 to 518 in d0a6649
This then means that the default doesn't match it in this block:
tools/nf_core/pipeline-template/lib/NfcoreSchema.groovy
Lines 538 to 540 in d0a6649
I wonder if we should just delete the first block (I don't think that should break anything, right?) and standardise that unset parameters should be defined as null in nextflow.config. I had a discussion with @drpatelh in Slack about this the other day I think too.
For the memory & time, I wonder if we just try and parse all strings as memory / time units - if it succeeds for both the param and the default we can save them as the correct unit and the default matching should work.