Missing dependency in orp_transrate Docker container

### Description of the bug Transrate fails to run from the suggested `orp_transrate` Docker container (`docker.io-avanibhojwani-orp_transrate-1.0.3_cv1.2.img`) due to missing BLAST in the container. There are 2 ways to solve this: 1. Build or find an `orp-transrate` container that has `blast` installed in the environment 2. Use the full [ORP Docker container](https://hub.docker.com/r/macmaneslab/orp) and make sure it activates the internal `orp` conda environment within the container and disable binding the `/home` folder (see below how I edited the `ORP_TRANSRATE` module to do that) ``` process ORP_TRANSRATE { tag "$meta.id" label 'process_high' // Using conda or the biocontainer for transrate results in a SNAP index error. // However, the error does not occur when using the tarball from the Oyster River Protocol. // see https://github.com/blahah/transrate/issues/248 // container 'docker.io/avanibhojwani/orp_transrate:1.0.3_cv1.2' container 'docker.io/macmaneslab/orp:2.3.3' containerOptions = '--no-mount /home' input: tuple val(meta), path(fasta) // assembly file tuple val(meta), path(reads) // processed reads path reference // reference proteins or transcripts fasta output: path "${fasta.baseName}/" , emit: transrate_results path "assemblies.csv" , emit: summary_csv path "transrate.log" , emit: log path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "ORP_TRANSRATE module does not support Conda. Please use Docker / Singularity / Podman instead." } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def reference = params.transrate_reference ? "--reference ${params.transrate_reference}" : "" """ source /home/orp/Oyster_River_Protocol/software/anaconda/install/bin/activate orp gunzip -c ${reads[0]} > ${prefix}_1.fq gunzip -c ${reads[1]} > ${prefix}_2.fq transrate \\ --assembly $fasta \\ --left ${prefix}_1.fq \\ --right ${prefix}_2.fq \\ --threads $task.cpus \\ $reference \\ $args cp .command.out transrate.log cp -r transrate_results/* ./ cat <<-END_VERSIONS > versions.yml "${task.process}": transrate: \$(transrate -v) END_VERSIONS """ } ``` ### Command used and terminal output ```console $ nextflow-24.04.4-all run nf-core/denovotranscript -r 1.1.0 \ --input Mnova_samplesheet.csv \ --transrate_reference /home/ibar/adna/sandbox/OTE14085/Minke_genome/ncbi_dataset/data/GCF_949987535.1/protein.faa \ --fasta /home/ibar/adna/sandbox/OTE14085/Mnova_genome/HumpbackWhale_Final_Genome_forNCBI.fasta \ --outdir assembly_results \ --assemblers trinity,rnaspades \ -with-tower \ -profile apptainer,bunya \ -c /home/ibar/.nextflow/bunya.config \ -resume Error executing process > 'NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE (pooled_reads)' Caused by: Process `NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE (pooled_reads)` terminated with an error exit status (1) Command executed: gunzip -c pooled_reads_1.merged.fastq.gz > pooled_reads_1.fq gunzip -c pooled_reads_2.merged.fastq.gz > pooled_reads_2.fq transrate \ --assembly all_assembled.okay.mrna \ --left pooled_reads_1.fq \ --right pooled_reads_2.fq \ --threads 12 \ --reference /home/ibar/adna/sandbox/OTE14085/Minke_genome/ncbi_dataset/data/GCF_949987535.1/protein.faa \ cp .command.out transrate.log cp -r transrate_results/* ./ cat <<-END_VERSIONS > versions.yml "NFCORE_DENOVOTRANSCRIPT:DENOVOTRANSCRIPT:TRANSRATE": transrate: $(transrate -v) END_VERSIONS Command exit status: 1 Command output: Dependencies are missing: - blastplus (2.2.[0-9]) You are running the packaged version of transrate This comes with the read-metrics dependencies pre-installed Command wrapper: Dependencies are missing: - blastplus (2.2.[0-9]) You are running the packaged version of transrate This comes with the read-metrics dependencies pre-installed Work dir: /scratch/project_mnt/S0016/sandbox/OTE14085/Mnova_denovotranscript_assembly/work/37/77c01c90c440f4d3b427ca1cddf9db ``` ### Relevant files _No response_ ### System information Nextflow version (eg. 24.04.4) Hardware: HPC Executor: slurm Container engine: Apptainer OS: Rocky Linux release 8.10 (Green Obsidian) Version of nf-core/denovotranscript: 1.1.0