2 fichiers modifiés avec 4 ajouts et 10 suppressions
+ 1
- 3
tasks/processSomatic.wdl
Voir le fichier
| String sample | String sample | ||||
| File varscan_snp | File varscan_snp | ||||
| File varscan_indel | File varscan_indel | ||||
| File ref_dir | |||||
| String fasta | |||||
| String docker | String docker | ||||
| String cluster_config | String cluster_config | ||||
| String disk_size | String disk_size |
+ 3
- 7
workflow.wdl
Voir le fichier
| input: | input: | ||||
| sample=sample_id, | sample=sample_id, | ||||
| varscan_snp=somatic.varscan_snp, | varscan_snp=somatic.varscan_snp, | ||||
| varscan_indel=somatic.varscan_indel, | |||||
| ref_dir=ref_dir, | |||||
| fasta=fasta, | |||||
| varscan_indel=somatic.varscan_indel, | |||||
| docker=varscan_docker, | docker=varscan_docker, | ||||
| disk_size=disk_size, | disk_size=disk_size, | ||||
| cluster_config=cluster_config | cluster_config=cluster_config | ||||
| varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc, | varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc, | ||||
| varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc, | varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc, | ||||
| varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc, | varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc, | ||||
| varscan_indel=somatic.varscan_indel, | |||||
| ref_dir=ref_dir, | |||||
| fasta=fasta, | |||||
| varscan_indel=somatic.varscan_indel, | |||||
| docker=varscan_docker, | docker=varscan_docker, | ||||
| disk_size=disk_size, | disk_size=disk_size, | ||||
| cluster_config=cluster_config | cluster_config=cluster_config | ||||
| } | } | ||||
| call annovar.annovar as snp_somatic_annovar { | call annovar.annovar as snp_somatic_annovar { | ||||
| input: | input: | ||||
| sample=sample_id, | sample=sample_id, |
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