snakemake-atac-seq issueshttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-atac-seq/-/issues2024-03-06T11:16:45+01:00https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-atac-seq/-/issues/6cleanup files / config / rules ununsed2024-03-06T11:16:45+01:00Aurélien Ginolhaccleanup files / config / rules ununsedlike bamtools filtering_rules.json, `sort_genomecov` etclike bamtools filtering_rules.json, `sort_genomecov` etcAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-atac-seq/-/issues/5rule `compute_matrix` should use `checkpoint` to parallelize the ref chunk2024-03-06T10:08:10+01:00Aurélien Ginolhacrule `compute_matrix` should use `checkpoint` to parallelize the ref chunkcheckpoints should replace the for loop here to parallelize this rule (right now takes 3h for 9 human samples)
https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#snakefiles-checkpointscheckpoints should replace the for loop here to parallelize this rule (right now takes 3h for 9 human samples)
https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#snakefiles-checkpointsAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-atac-seq/-/issues/4effective size of genome in rule `bigwig` should not be hardcoded hg382024-03-06T10:00:22+01:00Aurélien Ginolhaceffective size of genome in rule `bigwig` should not be hardcoded hg38`bamCoverage -b {input} -o {output} -p {threads} --effectiveGenomeSize 2805636331 --normalizeUsing RPGC``bamCoverage -b {input} -o {output} -p {threads} --effectiveGenomeSize 2805636331 --normalizeUsing RPGC`Aurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-atac-seq/-/issues/1genrich per replicates2021-09-21T13:28:19+02:00Aurélien Ginolhacgenrich per replicates