Accessible Workflow | Copy of Copy of imported: Trim-Align-Count-One-Condition-Paired -- with fixed tool params noodleds plus all unhidden

Galaxy Workflow ' Copy of Copy of imported: Trim-Align-Count-One-Condition-Paired -- with fixed tool params noodleds plus all unhidden'


StepAnnotation
Step 1: Input dataset collection
select at runtime
Step 2: FastQC
Output dataset 'output' from step 1
select at runtime
select at runtime
Step 3: Trimmomatic
Paired-end (as collection)
Output dataset 'output' from step 1
False
Trimmomatic Operations
Trimmomatic Operation 1
Sliding window trimming (SLIDINGWINDOW)
4
20
Step 4: HISAT2
FASTQ
Paired reads
Pair collection or list of pairs
Output dataset 'fastq_out_paired' from step 3
Use default values
False
False
Use a built-in genome
Not available.
Not available.
Not available.
False
Use default values
Use default values
Use default values
Specify spliced alignment parameters
0
12
Natural logarithm [f(x) = B + A * log(x)]
-8.0
1.0
Natural logarithm [f(x) = B + A * log(x)]
-8.0
1.0
20
500000
FR Unstranded
True
0
500
select at runtime
Report alignments tailored for transcript assemblers including StringTie.
Use default values
Use default job resource parameters
Step 5: StringTie
Output dataset 'output_alignments' from step 4
Do not use GFF/GTF
Use defaults
Use default job resource parameters
Step 6: htseq-count
Output dataset 'output_alignments' from step 4
Output dataset 'output_gtf' from step 5
Union
Yes
10
exon
gene_id
Do not output additional BAM file
False