Workflow Type: Galaxy
Open
Stable
No description specified
Inputs
ID | Name | Description | Type |
---|---|---|---|
library | library | runtime parameter for tool Cutadapt | n/a |
library | library | runtime parameter for tool Cutadapt | n/a |
reference_source | reference_source | runtime parameter for tool Map with BWA-MEM | n/a |
source | source | runtime parameter for tool gatk-RealignerTargetCreator | n/a |
source | source | runtime parameter for tool gatk-RealignerTargetCreator | n/a |
knownindels | knownindels | runtime parameter for tool gatk-RealignerTargetCreator | n/a |
source | source | runtime parameter for tool gatk-IndelRealigner | n/a |
source | source | runtime parameter for tool gatk-IndelRealigner | n/a |
known_sites | known_sites | runtime parameter for tool gatk-BaseRecalibrator | n/a |
source | source | runtime parameter for tool gatk-BaseRecalibrator | n/a |
source | source | runtime parameter for tool gatk-BaseRecalibrator | n/a |
source | source | runtime parameter for tool gatk-PrintReads | n/a |
source | source | runtime parameter for tool gatk-PrintReads | n/a |
source | source | runtime parameter for tool gatk-HaplotypeCaller | n/a |
source | source | runtime parameter for tool gatk-HaplotypeCaller | n/a |
Steps
ID | Name | Description |
---|---|---|
0 | cutadapt | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6 |
1 | BWA-MEM -> BAM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
2 | picard-MarkDuplicates | picard-MarkDuplicates |
3 | gatk-RealignerTargetCreator | gatk-RealignerTargetCreator |
4 | gatk-IndelRealigner | gatk-IndelRealigner |
5 | gatk-BaseRecalibrator | gatk-BaseRecalibrator |
6 | gatk-PrintReads | gatk-PrintReads |
7 | gatk-HaplotypeCaller | gatk-HaplotypeCaller |
Outputs
ID | Name | Description | Type |
---|---|---|---|
split_output | split_output | n/a | |
out1 | out1 | n/a | |
out2 | out2 | n/a | |
report | report | n/a | |
info_file | info_file | n/a | |
rest_output | rest_output | n/a | |
wild_output | wild_output | n/a | |
untrimmed_output | untrimmed_output | n/a | |
untrimmed_paired_output | untrimmed_paired_output | n/a | |
too_short_output | too_short_output | n/a | |
too_short_paired_output | too_short_paired_output | n/a | |
too_long_output | too_long_output | n/a | |
too_long_paired_output | too_long_paired_output | n/a | |
bam_output | bam_output | n/a | |
output | output | n/a | |
metrics | metrics | n/a | |
output | output | n/a | |
output | output | n/a | |
output | output | n/a | |
output | output | n/a | |
output | output | n/a |
Version History
Version 1 (earliest) Created 23rd Jul 2020 at 11:21 by Laura Rodriguez-Navas
Added/updated 1 files
Open
master
e438ba9

Creators
Not specifiedAdditional credit
Giacomo Tartari
Submitter
License
Activity
Views: 819 Downloads: 24
Created: 23rd Jul 2020 at 11:21
Last updated: 23rd Jul 2020 at 11:22
Last used: 23rd May 2022 at 05:34


None
