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lehtiolab / proteogenomics-analysis-workflow

IPAW: a Nextflow workflow for proteogenomics
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parameter issue #4

Closed nongbaoting closed 5 years ago

nongbaoting commented 5 years ago

I have encountered issue below, probably case by parameter normalpsms , but I don't set this value

$ nextflow run /public/home/nong/pro/proteogenomics/softs/proteogenomics-analysis-workflow/ipaw.nf   --tdb /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/varDB/VarDB.fasta   --mzmls "/public2/nong/project/proteogenomics-analysis-workflow/nong_temp/test_mzML/*.mzML"   --gtf /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/varDB/VarDB.gtf   --mods /public2/nong/project/proteogenomics-analysis-workflow/Mods.txt   --knownproteins /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/Homo_sapiens.GRCh38.pep.all.fa   --blastdb /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/UniProteome+Ensembl87+refseq+GENCODE24.proteins.fasta   --cosmic /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/cosmic/grch37_v85/CosmicMutantExport.tsv   --dbsnp /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/snp142CodingDbSnp.txt   --snpfa /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/varDB//MSCanProVar_ensemblV79.filtered.fasta   --genome /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/hg19_chromFaMasked/hg19.chr1-22.X.Y.M.fa.masked   --isobaric tmt10plex   --outdir results   -profile testing
N E X T F L O W  ~  version 0.31.1
Launching `/public/home/nong/pro/proteogenomics/softs/proteogenomics-analysis-workflow/ipaw.nf` [chaotic_fourier] - revision: ec952ef844
WARN: Access to undefined parameter `pisepdb` -- Initialise it to a default value eg. `params.pisepdb = some_value`
WARN: Access to undefined parameter `mzmldef` -- Initialise it to a default value eg. `params.mzmldef = some_value`
Detected setnames: NA
WARN: Access to undefined parameter `denoms` -- Initialise it to a default value eg. `params.denoms = some_value`
WARN: Access to undefined parameter `normalpsms` -- Initialise it to a default value eg. `params.normalpsms = some_value`
ERROR ~ Argument of `file` function cannot be null

 -- Check script 'ipaw.nf' at line: 118 or see '.nextflow.log' file for more details
[warm up] executor > local
[NA, /public2/nong/project/proteogenomics-analysis-workflow/nong_temp/varDB/VarDB.fasta]
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$msgfPlus = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$percolator = <value>` with a process selector
nongbaoting commented 5 years ago

I have found the the solution, using a older version old nextflow nextflow-0.29.0-all.

yafeng commented 5 years ago

it looks like $processName is no longer valid. can we fix the base.config file so it uses new syntax withLabel instead? @glormph https://www.nextflow.io/docs/latest/config.html#process-selectors

glormph commented 5 years ago

Could we use withName so we dont have to change anything else (and thus not put in extra labels)?

glormph commented 5 years ago

I pushed a commit for that, please try if it works!