Ngs qc qa workflow #6
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…es, fix dry run command
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In the next PR, let's rename the --pretend | -p option to --dry-run | -n.
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At some point, we are going to need a way to dynamically create this file on the fly. The current paths point to Biowulf HPC staff installations.
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Yeah that is partially the reason I chose to embed this conf file into the docker instead of use the one on the disk on biowulf. My original thought was to use common mount points, like /mnt/kaiju/... /mnt/kraken2... etc
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In the next PR, can you set latency-wait to 120 seconds?
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In the next PR, can we move to pulling threads information from a config file?
| adapters = get_adapter_opts, | ||
| container: "docker://rroutsong/dmux_ngsqc:0.0.1" | ||
| threads: 4 | ||
| resources: mem_mb = 8192 |
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Let's also pull mem_mb from a config file.
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With some of these commands, I ran separately through sbatch to get a feel for the resource requirements through the biowulf job dashboard, but I have not run everything thing. My plan here was to collect everything in a config once I had resolved the reqs for each rule.
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Do we need to prefix the commands with conda run -n ngsqc? Can move to having the conda env activate in the container (would require building it)?
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there is an ep.sh that should activate ngsqc on run, so it's either preface it with that or use the conda run. I believe that the singularity exec that snakemake uses overwrites the defined entrypoint for the image. The issue is activating an environment on initialization, so far nothing I have tried has worked to be able selectively activate a defined conda environment on image startup.
Workflow for FASTQ QC/QA pipeline including fastqc before and after trimming, fastp trimming, and fastq_screen contamination detection.