Closed ZaahidShaik closed 3 months ago
Dockerfile
nextflow.config
process { ..... ...... container = "" ...... ..... }
- Run the nextflow command using your VCF and HPO. ## My Test Output : - Tested with Both regular vcf and WGS vcf. - Run completed without issue.
Launching ./main.nf [desperate_escher] DSL2 - revision: b6ff1ac22e executor > local (14) [8b/fb28eb] process > INDEX_VCF [100%] 1 of 1 ✔ [ab/816b8a] process > VCF_PRE_PROCESS [100%] 1 of 1 ✔ [2d/a180c9] process > ANNOT_PHRANK [100%] 1 of 1 ✔ [df/8d07ec] process > ANNOT_ENSMBLE [100%] 1 of 1 ✔ [9e/53737a] process > TO_GENE_SYM [100%] 1 of 1 ✔ [79/17c7e7] process > PHRANK_SCORING [100%] 1 of 1 ✔ [91/ddaf87] process > HPO_SIM [100%] 1 of 1 ✔ [e4/4ae337] process > REMOVE_MITO_AND_UNKOWN_CHR [100%] 1 of 1 ✔ [ad/700573] process > FILTER_EXONIC [100%] 1 of 1 ✔ [b7/a7bdab] process > FILTER_PROBAND [100%] 1 of 1 ✔ [17/8dafb3] process > VEP_ANNOTATE [100%] 1 of 1 ✔ [56/57058d] process > FEATURE_ENGINEERING_PART1 [100%] 1 of 1 ✔ [70/fd765a] process > FEATURE_ENGINEERING_PART2 [100%] 1 of 1 ✔ [92/2e3365] process > PREDICTION [100%] 1 of 1 ✔ Completed at: 07-Aug-2024 16:30:58 Duration : 16m 36s CPU hours : 4.3 Succeeded : 14
./main.nf
Good job 👍
Change Report :
Testing step:
Dockerfile
.nextflow.config
underprocess { ..... ...... container = ""
......
.....
}
Launching
./main.nf
[desperate_escher] DSL2 - revision: b6ff1ac22e executor > local (14) [8b/fb28eb] process > INDEX_VCF [100%] 1 of 1 ✔ [ab/816b8a] process > VCF_PRE_PROCESS [100%] 1 of 1 ✔ [2d/a180c9] process > ANNOT_PHRANK [100%] 1 of 1 ✔ [df/8d07ec] process > ANNOT_ENSMBLE [100%] 1 of 1 ✔ [9e/53737a] process > TO_GENE_SYM [100%] 1 of 1 ✔ [79/17c7e7] process > PHRANK_SCORING [100%] 1 of 1 ✔ [91/ddaf87] process > HPO_SIM [100%] 1 of 1 ✔ [e4/4ae337] process > REMOVE_MITO_AND_UNKOWN_CHR [100%] 1 of 1 ✔ [ad/700573] process > FILTER_EXONIC [100%] 1 of 1 ✔ [b7/a7bdab] process > FILTER_PROBAND [100%] 1 of 1 ✔ [17/8dafb3] process > VEP_ANNOTATE [100%] 1 of 1 ✔ [56/57058d] process > FEATURE_ENGINEERING_PART1 [100%] 1 of 1 ✔ [70/fd765a] process > FEATURE_ENGINEERING_PART2 [100%] 1 of 1 ✔ [92/2e3365] process > PREDICTION [100%] 1 of 1 ✔ Completed at: 07-Aug-2024 16:30:58 Duration : 16m 36s CPU hours : 4.3 Succeeded : 14