These are chat archives for nextflow-io/nextflow

6th
Aug 2015
Sascha Steinbiss
@satta
Aug 06 2015 13:30
hmm... is it correct that the only difference between mix() and concat() is whether the order of items is conserved?
Paolo Di Tommaso
@pditommaso
Aug 06 2015 13:30
yes
Sascha Steinbiss
@satta
Aug 06 2015 13:30
okay, thanks!
Paolo Di Tommaso
@pditommaso
Aug 06 2015 13:31
welcome!
Sascha Steinbiss
@satta
Aug 06 2015 13:31
I'm trying to find out why a set of processes gets re-run all the time with seemingly the same input and -resume set
and I figure it might be some nondeterminism in the input files
Paolo Di Tommaso
@pditommaso
Aug 06 2015 13:31
I see
Sascha Steinbiss
@satta
Aug 06 2015 13:32
which are created by mix().collectFile()
Paolo Di Tommaso
@pditommaso
Aug 06 2015 13:32
well, but collectFile orders the file content
Sascha Steinbiss
@satta
Aug 06 2015 13:33
hmm
Paolo Di Tommaso
@pditommaso
Aug 06 2015 13:33
did you specify cache: 'deep' in that process ?
Sascha Steinbiss
@satta
Aug 06 2015 13:33
yes
Paolo Di Tommaso
@pditommaso
Aug 06 2015 13:34
you may try to check the collected file to see what differs
Sascha Steinbiss
@satta
Aug 06 2015 13:35
mapped_fasta.mix(mapped_fasta_ref).collectFile().set { full_mapped_fasta }
full_mapped_fasta.into{ full_mapped_fasta_for_index; full_mapped_fasta_for_query }

process blast_for_orthomcl_formatdb {
    cache 'deep'

    input:
    file 'mapped.fasta' from full_mapped_fasta_for_index

    output:
    file 'mapped.fasta' into full_mapped_fasta_indexed
    file 'mapped.fasta.phr' into full_mapped_fasta_indexed_phr
    file 'mapped.fasta.psq' into full_mapped_fasta_indexed_psq
    file 'mapped.fasta.pin' into full_mapped_fasta_indexed_pin

    """
    makeblastdb -dbtype prot -in mapped.fasta
    """
}

proteins_orthomcl_blast_chunk = full_mapped_fasta_for_query.splitFasta( by: 50, file: true)
process blast_for_orthomcl {
    cache 'deep'

    input:
    file 'mapped_chunk.fasta' from proteins_orthomcl_blast_chunk
    file 'mapped.fasta' from full_mapped_fasta_indexed.first()
    file 'mapped.fasta.phr' from full_mapped_fasta_indexed_phr.first()
    file 'mapped.fasta.psq' from full_mapped_fasta_indexed_psq.first()
    file 'mapped.fasta.pin' from full_mapped_fasta_indexed_pin.first()

    output:
    file 'blastout' into orthomcl_blastout

    """
   # blastp -word_size 6 -evalue 1e-5 -db mapped.fasta -outfmt 6 \
   #  -query mapped_chunk.fasta > blastout
    blastall -p blastp -W 4 -e 0.00001 -F T -d mapped.fasta -m 8 \
      -i mapped_chunk.fasta > blastout
    """
}
hmm ok will try that... hope I still have the log outputs around
Paolo Di Tommaso
@pditommaso
Aug 06 2015 13:36
ok