cwl workflow wrapping McCarroll lab dropseq analysis as described here:
Install prerequisites (this creates an Anaconda environment, downloads DropSeqTools, and installs TOIL/java/picard/STAR):
source create_environment_dropseq-cwl.sh
Ensure that the following directories are in your $PATH:
- bin/Drop-seq-tools
- bin/
- cwl/
- wf/
There is a bash script that wraps this workflow by doing the following:
- conveniently sets temporary/output directories
- generates logfiles
- runs the workflow using either cwl-runner or, if applicable, TOIL on either single or a cluster of machines.
By default, wf/dropseq-runner is set to 'cwltorq', which is set up to run PBS jobs on TSCC.
If not on TSCC, modify this wf/dropseq-runner file by changing the following line:
CWLRUNNER=cwltorq # either: cwltool cwltoil or cwltorq
to:
CWLRUNNER=cwltool # either: cwltool cwltoil or cwltorq (runs workflow with cwl-runner)
CWLRUNNER=cwltoil # either: cwltool cwltoil or cwltorq (runs workflow with singleMachine TOIL)
module load dropseqtools
- Visit this page and fill out the required fields: http://byee4.github.io/dropseq.html
- Copy and paste the contents of that form into a file (such as
samples.json), preferably inside a scratch directory. - Make this file executable (
chmod +x samples.json) - Assuming the above directories can be found on your path, you can run the workflow using the json file (
./samples.json)
Here are example outputs for a single sample:
| File name (run_id: r01, sample_id: s01) | Description of output |
|---|---|
| r01_s01.sam | Unaligned OUTPUT from picard FastqToSam |
| r01_s01.tagged1-12.bam | Unaligned tagged cell barcodes OUTPUT from TagBamWithReadSequenceExtended |
| r01_s01.tagged1-12.summary | Unaligned tagged cell barcodes SUMMARY from TagBamWithReadSequenceExtended |
| r01_s01.tagged1-12.tagged13-20.bam | Unaligned tagged UMI barcodes OUTPUT from TagBamWithReadSequenceExtended |
| r01_s01.tagged1-12.tagged13-20.summary | Unaligned tagged UMI barcodes SUMMARY from TagBamWithReadSequenceExtended |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.bam | Unaligned OUTPUT from TrimStartingSequence |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.summary | Unaligned OUTPUT_SUMMARY from TrimStartingSequence |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.bam | Unaligned OUTPUT from PolyATrimmer |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.summary | Unaligned OUTPUT_SUMMARY from PolyATrimmer |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARLog.out | Aligned STAR log file |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARLog.final.out | Aligned STAR final summary file |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARUnmapped.out.mate1 | Unaligned STAR sequences |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.bam | Aligned STAR file |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.namesorted.bam | OUTPUT from picard SortSam |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.namesorted.merged.bam | OUTPUT from picard MergeBamAlignment |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.namesorted.merged.TaggedGeneExon.bam | OUTPUT from TagReadWithGeneExon |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.namesorted.merged.TaggedGeneExon.synthesis_stats | OUTPUT_STATS from DetectBeadSynthesisErrors |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.namesorted.merged.TaggedGeneExon.synthesis_summary | SUMMARY from DetectBeadSynthesisErrors |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.namesorted.merged.TaggedGeneExon.cleaned.bam | OUTPUT from DetectBeadSynthesisErrors |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.namesorted.merged.TaggedGeneExon.cleaned.dge.summary.txt | SUMMARY from DigitalExpression |
| r01_s01.tagged1-12.tagged13-20.filtered.trimmed_smart.polyA_filtered.STARAligned.out.namesorted.merged.TaggedGeneExon.cleaned.dge.txt.gz | OUTPUT from DigitalExpression |
Macosko, Evan Z., et al. "Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets." Cell 161.5 (2015): 1202-1214.