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Output files

See original GitHub issue

In the Output Specification docs:

For more details, refer to the file table section in an HTML report generated by the pipeline. Files marked as (E) are outputs to be uploaded during ENCODE accession.

Which file is that comment referring to? I see 5 html files in the output of the pipeline:

call-ataqc/shard-0/execution/ALS-29-ISO_diMN18_rep1_1.fastq.trim.merged_qc.html
call-ataqc/shard-0/execution/glob-47eccad02a94d57a391dcc7587d65007/ALS-29-ISO_diMN18_rep1_1.fastq.trim.merged_qc.html
call-qc_report/execution/glob-eae855c82d0f7e2185388856e7b2cc7b/qc.html
call-qc_report/execution/qc.html
call-qc_report/inputs/-305557727/ALS-29-ISO_diMN18_rep1_1.fastq.trim.merged_qc.html

I would anticipate that the comment referred to

call-qc_report/execution/qc.html

but when I open that HTML in my browser, there’s no section for output files. qc.json also has no output files listed.

My real issue is I’m trying to capture the outputs of this pipeline. Is it safe to assume the output files are always under /execution but not under /glob-*?

Thanks,

Issue Analytics

State:
Created 4 years ago
Comments:5 (3 by maintainers)

Top GitHub Comments

2reactions

leepc12commented, Apr 18, 2019

call-reproducibility_overlap/execution/optimal_peak.narrowPeak.bb

0reactions

alexlenailcommented, Apr 18, 2019

@leepc12 So if I only look at one peak file, as the output of the entire pipeline, which file should it be?

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