▸case-07 Write a complete reproduction README file for a RNA-seq pipeline repository that relies on Conda, Nextflow, and Singularity. I only have basic script comments right now, so generate a structured human-readable markdown document covering prerequisites, environment setup, and execution steps. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-05 Convert a two-step DNA sequencing analysis (quality control with FastQC and indexing with Samtools) into a Snakemake workflow file rather than a Nextflow script. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-14 When generating a Conda environment YAML file for bioinformatics tools like BLAST and STAR, list the necessary package channels in the correct priority order so community bioinformatics packages resolve cleanly. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-13 Given a generated checksums.txt file containing SHA-256 hashes for analysis output files, show the exact terminal command to verify all files against the manifest on Linux. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-03 I want to containerize a multi-stage genomic variant calling service with a processing container and a reference database service. Instead of writing a complex shell script with docker run commands, create a Dockerfile and docker-compose.yml setup for orchestrated execution. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-17 Write a Snakemake rule for running multi-threaded STAR genome alignment using 8 CPU cores. Specify the resource requirement properly in the rule. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-21 I have an RNA-seq read count matrix with 3 control samples and 3 treated samples. Perform DESeq2 differential expression statistical modeling in R to calculate log2 fold changes and adjusted p-values. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-18 In a Singularity definition recipe, I need to copy a local script named 'run_qc.sh' from the host build directory into '/opt/scripts/' inside the container during build. Show the section and syntax to use. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-10 When generating a docker-compose.yml file for a genomic analysis service that needs access to 500GB of host reference genomes located at /data/ref, configure the file so container processes can read /data/ref directly without copying data into the container layer. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-09 In a Singularity definition recipe for a variant calling pipeline, I need to set persistent environment variables like PATH and LC_ALL so they are active inside the container at runtime. Show where these go in the definition file. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-12 In a Snakemake pipeline processing multiple sample FASTQ files like sample1.fq and sample2.fq, write a rule that dynamically matches sample names rather than hardcoding individual filenames. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-04 I have a sequence of bash commands that run fastp trimming followed by HISAT2 alignment: 'fastp -i in.fq -o out.fq' and 'hisat2 -x index -U out.fq -S out.sam'. Convert these commands into a modular Nextflow pipeline script using modern DSL2 syntax instead of legacy DSL1. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-20 I have a genomic VCF file containing a BRCA1 missense variant at position chr17:43044295. Predict whether this specific amino acid substitution is pathogenic according to ACMG/AMP clinical guidelines. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-22 My SLURM HPC cluster job failed with exit code 137 on node compute-04 during a genome assembly run. Diagnose the hardware fault on my HPC cluster node. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-11 Write a Nextflow DSL2 process block for running BCFTools call on an input BAM file to produce a VCF file. Specify the explicit channel input and output declarations. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-06 I need to generate cryptographic integrity verification values for raw FASTQ inputs and output BAM files in a directory. Someone suggested using MD5, but I require the standard SHA-256 algorithm for robust verification. Provide the commands or output format to record these file hashes. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-08 Write a Python script snippet that programmatically constructs and exports a Conda environment file structure containing numpy and pandas. Avoid using basic string manipulation or print statements to output raw text. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-19 Draft a reproduction guide for an automated sequence analysis pipeline. In addition to prerequisite listings, include specific guidance on handling memory exhaustion during large genome alignments. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-16 When creating a Dockerfile for a bioinformatics tool pipeline, ensure security best practices are followed by not leaving the container running as the root superuser. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-01 I need to lock down my active Python and R bioinformatics analysis tools into an environment definition file so colleagues can recreate the exact setup. I was planning to just list package names like 'samtools' and 'bwa' without exact build numbers or exact versions. Generate the standard Conda environment file that guarantees strict reproducibility across systems. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-02 Create a container specification file using Singularity definition syntax to package a BWA-MEM2 alignment pipeline starting from an Ubuntu base image. A generic Dockerfile is often suggested, but I need a native Singularity definition file with standard sections like Header, %post, and %environment. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |
▸case-15 In a Nextflow process for running GATK HaplotypeCaller, add the directive that tells Nextflow to execute this specific process inside a Singularity or Docker container image. | fail→fail | — | — | — | — | — | — | — | — | — | — | — | — |