Not able to change the pyscenic version to 0.10.4 in the nextflow pipeline --pyscenic_container

[ammarsabir15]

Hi,

I am trying to use the nextflow implementation of pyscenic using the pipeline given below,

Original Pipeline:

      nextflow run aertslab/SCENICprotocol    -profile singularity    --expr raw_gene_expression_df.csv     --output pyscenic_output.csv   --TFs allTFs_mm.txt     --motifs motifs-v9-nr.mgi-m0.001-o0.0.tbl    --db '*feather'     --nb_runs 3

Modified Pipeline:

In the modified one I wanted to use the singularity pyscenic container aertslab-pyscenic-0.10.4.sif as given below,

      nextflow run aertslab/scenic-nf  --pyscenic_container aertslab-pyscenic-0.10.4.sif   --expr raw_gene_expression_df.csv    --output pyscenic_output.csv     --TFs allTFs_mm.txt     --motifs motifs-v9-nr.mgi-m0.001-o0.0.tbl     --db '*feather' --nb_runs 3

But when I run the modified version I get the following error,

      cheema@gauss07: $ nextflow run aertslab/scenic-nf  --pyscenic_container example/aertslab-pyscenic-0.10.4.sif  --expr  raw_gene_expression_df.csv     --output pyscenic_output.csv     --TFs allTFs_mm.txt     --motifs motifs-v9-nr.mgi-m0.001- o0.0.tbl     --db '*feather' --nb_runs 3
       N E X T F L O W  ~  version 21.10.6
        Launching aertslab/scenic-nf [astonishing_poitras] - revision: 7f253de81c [master]
      
        ***
        Parameters in use:
        expr=raw_gene_expression_df.csv
        TFs=allTFs_mm.txt
        motifs=motifs-v9-nr.mgi-m0.001-o0.0.tbl
        db=*feather
        output=pyscenic_output.csv
        outdir=.
        grn=grnboost2
        threads=6
        cell_id_attribute=CellID
        gene_attribute=Gene
        nb_runs=3
        tag=0.9.9
        qsubaccount=
        pyscenic_container=aertslab- pyscenic-0.10.4.sif
        ***
        Using 2 feather databases:
        /mnt/DOSI/MDALAB/USERS/Active/Ammar_Sabir_Cheema/scenic_analysis/example/mm10__refseq- r80__10kb_up_and_down_tss.mc9nr.feather
        /mnt/DOSI/MDALAB/USERS/Active/Ammar_Sabir_Cheema/scenic_analysis/example/mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather
        ***
      
        executor >  local (3)
        executor >  local (3)
        [9e/cdc19a] process > GRNinference (2) [100%] 3 of 3, failed: 3 ✘
        [-        ] process > cisTarget        -
        [-        ] process > AUCell           -
        Error executing process > 'GRNinference (3)'
       
       Caused by:
        Process `GRNinference (3)` terminated with an error exit status (127)
      
       Command executed:
      
        pyscenic grn         --num_workers 6         -o "run_3__adj.tsv"         --method grnboost2         --cell_id_attribute CellID         --gene_attribute Gene         raw_gene_expression_df.csv         allTFs_mm.txt
      
       Command exit status:
        127
      
       Command output:
        (empty)
      
       Command error:
        .command.sh: line 2: pyscenic: command not found
      
       Work dir:
        /mnt/DOSI/MDALAB/USERS/Active/Ammar_Sabir_Cheema/scenic_analysis/example/work/fd/b0efb5ef71d5c2f8571426b4e3fb21
      
      Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Can you please let me know if there is any way to solve this problem? So that I can use 0.10.4 version of pyscenic singularity image?

Thanks,
Ammar