hashing demultiplexing pipeline errors

[michaelplynch]

Hello! I'm trying to run the hadge pipeline (v0.2.0) and am running into issues with the hashing demultiplexing side using conda. Wondering is this part of the pipeline considered stable? Using Nextflow v24.04.2 with nextflow.config file attached as .txt (Github doesn't allow .config extension nextflow.config.txt apparently). As an FYI there looks to be other errors within methods I have currently set to false caused by python package updates e.g. https://stackoverflow.com/questions/78090426/cannot-import-name-binom-test-from-scipy-stats-error-when-using-borutashap and https://stackoverflow.com/questions/78634235/numpy-dtype-size-changed-may-indicate-binary-incompatibility-expected-96-from that may cause users issues also. Should be fixable by setting the package version to pre- these changes.

Command: nextflow run main.nf -profile test,conda_singularity --mode rescue Output: WARN: Input tuple does not match tuple declaration in process HADGE:run_multi:hash_demultiplexing:summary` -- offending value: [hadge, null, /data/projects/demuxSNP/hadge-0.2.0/work/9b/f888d95da8ec8b85c433f84e0c5125/multiseq_hadge, /data/projects/demuxSNP/hadge-0.2.0/work/d0/35e8330ab4ff4e1b68bd66dcb739e3/htodemux_hadge, null, null] ERROR ~ Error executing process > 'HADGE:run_multi:hash_demultiplexing:summary (2)'

Caused by: No such variable: demuxem_res -- Check script 'modules/multi/hash_demultiplexing.nf' at line: 39

Source block: def htodemux_files = "" def hashsolo_files = "" def multiseq_files = "" def hashedDrops_files = "" def gmmDemux_files = "" def demuxem_files = "" def bff_files = "" def generate_adata = "" def generate_mdata = "" if (demuxem_result != "no_result"){ demuxem_files = "--demuxem ${demuxem_res}" } if (hashsolo_result != "no_result"){ hashsolo_files = "--hashsolo ${hashsolo_res}" } if (htodemux_result != "no_result"){ htodemux_files = "--htodemux ${htodemux_res}" } if (multiseq_result != "no_result"){ multiseq_files = "--multiseq ${multiseq_res}" } if (hashedDrops_result != "no_result"){ hashedDrops_files = "--hashedDrops ${hashedDrops_res}" } if (gmmDemux_result != "no_result"){ gmmDemux_files = "--gmm_demux ${gmmDemux_res}" } if (bff_result != "no_result"){ bff_files = "--bff ${bff_res}" } if (generate_anndata == "True"){ if(rna_matrix.name == "None"){ error "Error: RNA count matrix is not given." } generate_adata = "--generate_anndata --read_rna_mtx rna_data" } if (generate_mudata == "True"){ if(rna_matrix.name == "None"){ error "Error: RNA count matrix is not given." } if(hto_matrix.name == "None"){ error "Error: HTO count matrix is not given." } generate_mdata = "--generate_mudata --read_rna_mtx rna_data --read_hto_mtx hto_data" } """ summary_hash.py $demuxem_files $htodemux_files $multiseq_files $hashedDrops_files $hashsolo_files $gmmDemux_files $bff_files $generate_adata $generate_mdata """

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details`