Introduction
Script
Input
Output
cactus_align
Introduction
The second step of the process after the completion of preprocess.
Script
Input
| Task name | Attribute name | Type | Description |
|---|---|---|---|
| * cactus_step3.cactus_align | out_hal_name | String | Output HAL file |
| * cactus_step3.cactus_align | out_fa_name | String | Output fasta file |
| * cactus_step3.cactus_align | in_root | String | Name of ancestral node (which must appear in NEWICK tree in <seqfile>) to use as a root for the alignment.Any genomes not below this node in the tree may be used as outgroups but will never appear in the output.if no root is specifed then the root of the tree is used. |
| * cactus_step3.cactus_align | in_fa_names | Array[String] | names (must be same number as --in_fa_files) of path overrides |
| * cactus_step3.cactus_align | in_fa_files | Array[File] | paths (multiple allowed) to override from seqFile |
| * cactus_step3.cactus_align | in_blast_files | Array[File] | Blast output file list(from cactus-blast) |
| * cactus_step3 | seq_file | File | Seq file |
| cactus_step3 | memory | String | Number of memory running tasksnotice:1. The value range is 0.25-32 cores, in addition, 48 cores and 64 cores can be selected, and the CPU must be an integer multiple of 0.25 cores; 2. The memory value range is 1GB-512GB, and the memory must be an integer multiple of 1GB. 3. The CPU / memory ratio must be between 1:2 and 1:8 |
| cactus_step3 | cpu | String | Number of CPU running tasks.notice:1. The value range is 0.25-32 cores, in addition, 48 cores and 64 cores can be selected, and the CPU must be an integer multiple of 0.25 cores; 2. The memory value range is 1GB-512GB, and the memory must be an integer multiple of 1GB. 3. The CPU / memory ratio must be between 1:2 and 1:8 |
| cactus_step3 | config_file | File | Specify cactus configuration file |
Output
| Task name | Attribute name | Type | Description |
|---|---|---|---|
| * cactus_step3 | out_hal | File | output Hierarchical Alignment (HAL) Format file list.return the output file to the column name of the corresponding table by this.xxx |
| * cactus_step1 | out_fa | File | output FASTA Format file .return the output file to the column name of the corresponding table by this.xxx |