Can't run all the pipeline steps, but I don't have any errors reported

[janamace]

Hello, I'm trying to apply the pipeline using the command:

NXF_VER=22.10.0 nextflow run /mnt/d/proteogenomics-analysis-workflow-master/main.nf
--tdb /mnt/d/varDB/VarDB.fasta
--mzmldef /mnt/d/Test_01/mzml/spectra_file_list.txt
--activation hcd
--gtf /mnt/d/Test_01/varDB_gtf/VarDB.gtf
--mods /mnt/d/Test_01/mods/Mods.txt
--knownproteins /mnt/d/Test_01/known_prot/Homo_sapiens.GRCh38.pep.all.fa
--blastdb /mnt/d/Test_01/blastdb/UniProteome+Ensembl87+refseq+GENCODE24.proteins.fasta
--snpfa /mnt/d/snpfa/MSCanProVar_ensemblV79.filtered.fasta
--genome /mnt/d/hg19_masked/hg19.chr1-22.X.Y.M.fa.masked
--dbsnp /mnt/d/SNPDb/snp142CodingDbSnp.txt
--annovar_dir /mnt/d/annovar
--bigwigs /mnt/d/bigwigs
--outdir /mnt/d/Test_01/results
-profile docker
-with-report pipeline_report.html
-with-trace

I have six mzML files with label-free quantification. My report files (.html and .log) show that the following steps were executed and completed:

prepareFilterDB
createNewSpectraLookup
concatFasta
msgfPlus (1-8)
percolator

However, the output shows that the following processes did not execute:

splitSetNormalSearchPsms
splitPlateNormalSearchPsms
normalSearchPsmsToPeptides
create6FTDB
IsobaricQuant
getVariantPercolator
getNovelPercolator
filterPercolator
svmToTSV
createPSMTable
mergeSetPSMtable
prePeptideTable
createFastaBedGFF
BlastPNovel
ParseBlastpOut
ValidateSingleMismatchNovpeps
novpepSpecAIOutParse
BLATNovel
parseBLATout
labelnsSNP
phastcons
phyloCSF
scanBams
annovar
parseAnnovarOut
combineResults
prepSpectrumAI
SpectrumAI
mapVariantPeptidesToGenome
mergeSetPeptidetable

The only output file I have is quant_lookup.sql.

I tried changing the nextflow.config file to:

params {
container = 'lehtiolab/ipaw:0.5' // Container slug. Stable releases should specify release tag!
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
awsqueue = false
awsregion = 'eu-west-1'
external_config_version = 'master'

pisepdb = false
isobaric = false
activation = 'hcd'
bamfiles = false
mods = true
knownheaders = true
novheaders = true
varheaders = true
saavheader = true
noclassfdr = false
dbsnp = true
cosmic = false
mzmldef = true
input = false
normalpsms = false
annovar_dir = true
bigwigs = true
splitchar = true
quantlookup = false
minlen = 8
maxlen = 50
maxmiscleav = 0

}

But it doesn't seem to produce the expected outputs.

Could someone help me? I'm very new to these applications and may be missing something.

Thanks!