All output filenames keep prefixes from corresponding input filenames. For example. If you have started from REP1.fastq.gz and REP2.fastq.gz then corresponding alignment log for each replicate has a filename of REP1.flagstat.qc and REP2.flagstat.qc, respectively.
Final HTML report (qc.html) and QC json (qc.json) files do not have any prefix.
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DNAnexus: Output will be stored on the specified output directory without any subdirectories. -
Cromwell:Cromwellwill store outputs for each task undercromwell-executions/[WORKFLOW_ID]/call-[TASK_NAME]/shard-[IDX]. For all tasks except two peak calling tasksidr(irreproducible discovery rate) andoverlap(naive overlapping peaks),[IDX]means a zero-based index for each replicate. For two tasksidrandoverlap,[IDX]stands for a zero-based index for all possible pair of replicates. For example, you have 3 replicates and all possible combination of two replicates are[(rep1,rep2), (rep1,rep3), (rep2,rep3)]. Therefore,call-idr/shard-2should be an output directory for the pair of replicate 2 and 3.
There can be duplicate output files on execution/ and execution/glob-*/ directories. A file on the latter (execution/glob-*/) is a symbolic link of an actual output file on the former. For Google Cloud Storage bucket (gs://) there is no execution/ directory and files on glob-*/ are actual outputs.
| task | filename | description |
|---|---|---|
| merge_fastq | merge_fastqs_R?_*.fastq.gz | Merged FASTQ |
| trim_fastq | *.trim_*bp.fastq.gz | Trimmed FASTQ (R1 only) |
| bwa | * .bam | Raw BAM |
| bwa | * .bai | BAI for Raw BAM |
| bwa | * .flagstat.qc | Samtools flagstat log for raw BAM |
| filter | * .nodup.bam | Filtered/deduped BAM |
| filter | * .nodup.flagstat.qc | Samtools flagstat log for filtered/deduped BAM |
| filter | * .dup.qc | Picard/sambamba markdup log |
| filter | * .pbc.qc | PBC QC log |
| bam2ta | * .tagAlign.gz | TAG-ALIGN generated from filtered BAM |
| bam2ta | * .N.tagAlign.gz | Subsampled (N reads) TAG-ALIGN generated from filtered BAM |
| bam2ta | * .tn5.tagAlign.gz | TN5-shifted TAG-ALIGN |
| spr | * .pr1.tagAlign.gz | 1st pseudo-replicated TAG-ALIGN |
| spr | * .pr2.tagAlign.gz | 2nd pseudo-replicated TAG-ALIGN |
| pool_ta | * .tagAlign.gz | Pooled TAG-ALIGN from all replciates |
| fingerprint | * .jsd.qc | DeepTools fingerprint log |
| fingerprint | * .png | DeepTools fingerprint plot |
| choose_ctl | ctl_for_rep*.tagAlign.gz | Chosen control for each IP replicate |
| xcor | * .cc.plot.pdf | Cross-correlation plot PDF |
| xcor | * .cc.plot.png | Cross-correlation plot PNG |
| xcor | * .cc.qc | Cross-correlation analysis score log |
| xcor | * .cc.fraglen.txt | Estimated fragment length |
| macs2 | * .narrowPeak.gz | NARROWPEAK |
| macs2 | * .bfilt.narrowPeak.gz | Blacklist-filtered NARROWPEAK |
| macs2 | * .bfilt.narrowPeak.bb | Blacklist-filtered NARROWPEAK in BigBed format |
| macs2 | * .pval.signal.bigwig | p-val signal BIGWIG |
| macs2 | * .fc.signal.bigwig | fold enrichment signal BIGWIG |
| macs2 | * .frip.qc | Fraction of read (TAG-ALIGN) in peaks (NARROWPEAK) |
| spp | * .regionPeak.gz | SPP NARROWPEAK(REGIONPEAK) |
| spp | * .bfilt.regionPeak.gz | Blacklist-filtered REGIONPEAK |
| spp | * .bfilt.regionPeak.bb | Blacklist-filtered REGIONPEAK in BigBed format |
| spp | * .frip.qc | Fraction of read (TAG-ALIGN) in peaks (REGIONPEAK) |
| idr | * .*Peak.gz | IDR NARROWPEAK |
| idr | * .bfilt.*Peak.gz | Blacklist-filtered IDR NARROWPEAK |
| idr | * .bfilt.*Peak.bb | Blacklist-filtered IDR NARROWPEAK in BigBed format |
| idr | * .txt.png | IDR plot PNG |
| idr | * .txt.gz | Unthresholded IDR output |
| idr | * .log | IDR STDOUT log |
| idr | * .frip.qc | Fraction of read (TAG-ALIGN) in peaks (IDR NARROWPEAK) |
| overlap | * .*Peak.gz | Overlapping NARROWPEAK |
| overlap | * .bfilt.*Peak.gz | Blacklist-filtered overlapping NARROWPEAK |
| overlap | * .bfilt.*Peak.bb | Blacklist-filtered overlapping NARROWPEAK in BigBed format |
| overlap | * .frip.qc | Fraction of read (TAG-ALIGN) in peaks (overlapping NARROWPEAK) |
| reproducibility | * .reproducibility.qc | Reproducibililty QC log |
| reproducibility | optimal_peak.gz | Optimal final peak file |
| reproducibility | optimal_peak.bb | Optimal final peak file in BigBed format |
| reproducibility | conservative_peak.gz | Conservative final peak file |
| reproducibility | conservative_peak.bb | Conservative final peak file in BigBed format |
| qc_report | qc.html | Final HTML QC report |
| qc_report | qc.json | Final QC JSON |