Transfered fragments (imported from uploaded file)


StepAnnotation
Step 1: Input dataset
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset
select at runtime
Step 4: Input dataset
select at runtime
Step 5: Map with BWA-MEM
Use a genome from history and build index
Output dataset 'output' from step 1
Auto. Let BWA decide the best algorithm to use
Paired
Output dataset 'output' from step 2
Output dataset 'output' from step 3
Empty.
Do not set
1.Simple Illumina mode
Use default job resource parameters
Step 6: BAM-to-SAM
Output dataset 'bam_output' from step 5
Nothing selected.
Align_Ref1
Step 7: Flagstat
Output dataset 'bam_output' from step 5
Step 8: Select
Output dataset 'output1' from step 6
NOT Matching
NM:i:0
Mismatch_Ref1
Step 9: Select
Output dataset 'output1' from step 6
Matching
NM:i:0
Match_Ref1
Step 10: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/drosofff/sam_to_fastq/sam_to_fastq/0.1'
Step 11: SAM-to-BAM
Use a genome from the history
Output dataset 'out_file1' from step 8
Output dataset 'output' from step 1
Use default job resource parameters
Step 12: SAM-to-BAM
Use a genome from the history
Output dataset 'out_file1' from step 9
Output dataset 'output' from step 1
Use default job resource parameters
Step 13: Map with BWA-MEM
Use a genome from history and build index
Output dataset 'output' from step 4
Auto. Let BWA decide the best algorithm to use
Single
Output dataset 'output' from step 10
Set read groups (SAM/BAM specification)
False
Reads
False
Reads
ILLUMINA
False
Reads
Empty.
Empty.
Empty.
Empty.
Empty.
Empty.
Not available.
Empty.
1.Simple Illumina mode
Use default job resource parameters
Step 14: Flagstat
Output dataset 'output1' from step 11
Step 15: Flagstat
Output dataset 'output1' from step 12
Step 16: BAM-to-SAM
Output dataset 'bam_output' from step 13
Nothing selected.
Align_Ref2
Step 17: Flagstat
Output dataset 'bam_output' from step 13
Step 18: Select
Output dataset 'output1' from step 16
NOT Matching
NM:i:0
Mismatch_Ref2
Step 19: Select
Output dataset 'output1' from step 16
Matching
NM:i:0
Match_Ref2
Step 20: SAM-to-BAM
Use a genome from the history
Output dataset 'out_file1' from step 18
Output dataset 'output' from step 4
Use default job resource parameters
Step 21: SAM-to-BAM
Use a genome from the history
Output dataset 'out_file1' from step 19
Output dataset 'output' from step 4
Use default job resource parameters
Step 22: Flagstat
Output dataset 'output1' from step 20
Step 23: Flagstat
Output dataset 'output1' from step 21