Integrate snakemake provenance data

[adknaupp]

By default, Snakemake writes provenance data JSON for every(?) output file. By passing an option snakemake --persistence-backend db [--persistence-backend-db-url URL], you can send that data to "any database backend supported by SQLAlchemy".

Let's add a dummy (or real) DB service dedicated to receiving these messages on the workstation. The question is how to do auth. Hopefully there's a better option than SSH.

{
   "record_format_version":6,
   "code":"\n        mkdir -p {wildcards.out_ribo}/logs/riboseqc_{wildcards.tar}/\n        bash riboseqc {input.mapped} {params.out_prefix} &> {output} || true\n        if [ -f {params.indir}/{wildcards.sample}.bam_RiboseQC_report.html ]; then\n            mv {params.indir}/{wildcards.sample}.bam_RiboseQC_report.html {params.out_prefix}_riboseqc.html\n            # mv {params.indir}/{wildcards.sample}*.bedgraph {wildcards.out_ribo}/logs/riboseqc/\n            rm -r {params.indir}/{wildcards.sample}*.html_plots\n            rm {params.indir}/{wildcards.sample}*.txt\n        fi\n        ",
   "rule":"run_riboseqc",
   "input":[
      "containers/riboseqc.sif",
      "out/ribo/mapped_STD_TS/_bams/HFF_P001_mock_2.bam"
   ],
   "log":[
      
   ],
   "params":[
      "'out/ribo/mapped_STD_TS/_bams/'",
      "'out/ribo/mapped_STD_TS/riboseqc/HFF_P001_mock_2'"
   ],
   "shellcmd":"\n        mkdir -p out/ribo/logs/riboseqc_STD_TS/\n        bash riboseqc out/ribo/mapped_STD_TS/_bams/HFF_P001_mock_2.bam out/ribo/mapped_STD_TS/riboseqc/HFF_P001_mock_2 &> out/ribo/logs/riboseqc_STD_TS/HFF_P001_mock_2.txt || true\n        if [ -f out/ribo/mapped_STD_TS/_bams//HFF_P001_mock_2.bam_RiboseQC_report.html ]; then\n            mv out/ribo/mapped_STD_TS/_bams//HFF_P001_mock_2.bam_RiboseQC_report.html out/ribo/mapped_STD_TS/riboseqc/HFF_P001_mock_2_riboseqc.html\n            # mv out/ribo/mapped_STD_TS/_bams//HFF_P001_mock_2*.bedgraph out/ribo/logs/riboseqc/\n            rm -r out/ribo/mapped_STD_TS/_bams//HFF_P001_mock_2*.html_plots\n            rm out/ribo/mapped_STD_TS/_bams//HFF_P001_mock_2*.txt\n        fi\n        ",
   "incomplete":false,
   "starttime":null,
   "endtime":1774363365.585184,
   "job_hash":1427555499574,
   "conda_env":null,
   "software_stack_hash":"2cbf871cb1c51f8e57e01dd71d175f77",
   "container_img_url":"containers/riboseqc.sif",
   "input_checksums":{
      
   }
}