Workflow: Coinami
Coinami is designed and developed by a small group in Bilkent University
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
reads_1 | File |
First strand reads from Illumina Sequence |
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reads_2 | File |
Second strand reads from Illumina Sequence |
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reference | File |
Reference file to start processing |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
alignment_1 |
bwa-mem.cwl
(CommandLineTool)
|
Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq] |
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alignment_2 |
samtools-view.cwl
(CommandLineTool)
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samtools-view.cwl is developed for CWL consortium
Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...] |
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alignment_3 |
samtools-sort.cwl
(CommandLineTool)
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samtools-sort.cwl is developed for CWL consortium
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or
-T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)
-@ INT Set number of sorting and compression threads [1] |
|
alignment_4 |
samtools-rmdup.cwl
(CommandLineTool)
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samtools-rmdup.cwl is developed for CWL consortium |
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alignment_5 |
samtools-index.cwl
(CommandLineTool)
|
samtools-index.cwl is developed for CWL consortium |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
output | File |
Final output after removing duplicates |
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indexed_output | File |
Index of final output |
https://w3id.org/cwl/view/git/52ff36dc9cd73daacbc151ab6562f46dd7587770/coinami.cwl