CNV consensus w freec wxs

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

What was your approach?

This PR adds back the missing scripts from the focal-cn module bash script, creates an WXS only freec file, and creates an output consensus using freec wxs.

What GitHub issue does your pull request address?

Closes #589

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

This takes quite some time to run ~4 hours or so

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

yes

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jharenza]

@rjcorb result file md5sums:

348e2ab8d9f043f9dbd20116ec573538  cnvkit_annotated_cn_wxs_autosomes.tsv.gz
2caf1bebfcc0f8d0286d90aff14071f7  cnvkit_annotated_cn_wxs_autosomes_unresolved.tsv.gz
2c4e47c30fdb19464850520ddc72f2aa  cnvkit_annotated_cn_wxs_x_and_y.tsv.gz
ca0b80ab66b0785bcb86e2bab0be0908  cnvkit_annotated_cn_wxs_x_and_y_unresolved.tsv.gz
b398a60df88c5d3d60e9620a7e35b0f4  cnvkit_with_status.tsv
d106d5fe2dcbd74d83bbfdbaf6233ab6  consensus_seg_annotated_cn_autosomes.tsv.gz
2856bcc22b7a2b9ab99024482a6a1e27  consensus_seg_annotated_cn_autosomes_unresolved.tsv.gz
7646933dc26a72188ffd7351db90842b  consensus_seg_annotated_cn_x_and_y.tsv.gz
bd8ee1367666f5195fb2436d5886779f  consensus_seg_annotated_cn_x_and_y_unresolved.tsv.gz
9d5c84ad86a8a53a9a824e8db4fea351  consensus_seg_focal_cn_recurrent_genes.tsv
6f24498ec1b73c9c274fe742f89ef28c  consensus_seg_most_focal_cn_status.tsv.gz
93f7bf63140e2f319cd39d3412ee8126  consensus_seg_recurrent_focal_cn_units.tsv
132aade88a062ad5b6d834c717d3c74a  consensus_seg_with_status.tsv
ebf28bc334493a146075298eac1ef6c6  consensus_seg_with_ucsc_cytoband_status.tsv.gz
13999947b24a6c536a52f359d646d542  consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only.tsv.gz
5290b062244643dcb89b3de494632961  consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_autosomes.tsv.gz
c3e85a8e072d54c45b128b38daa49a7f  consensus_wgs_plus_cnvkit_wxs_plus_freec_tumor_only_x_and_y.tsv.gz
0651fd84b72dd82228ebdb304ffbdccd  consensus_wgs_plus_freec_wxs_plus_freec_tumor_only.tsv.gz
522c08c02484321909a7d7ec25eeb3c7  consensus_wgs_plus_freec_wxs_plus_freec_tumor_only_autosomes.tsv.gz
973355320ae9779f8898d9acee8c20fe  consensus_wgs_plus_freec_wxs_plus_freec_tumor_only_x_and_y.tsv.gz
6b1c7138f15df2a86f74670d92063c98  controlfreec_annotated_cn_autosomes.tsv.gz
0430dcffd9b0999f284f5f7c78fba9e3  controlfreec_annotated_cn_autosomes_unresolved.tsv.gz
92f77d9e1768d12e2d76b2eac656fa38  controlfreec_annotated_cn_wxs_autosomes.tsv.gz
fe81628f29bda32a9f853f8f5131215c  controlfreec_annotated_cn_wxs_autosomes_unresolved.tsv.gz
9280fceb46423131d03f8c14e64da571  controlfreec_annotated_cn_wxs_x_and_y.tsv.gz
c0158260bde52cb214c0b15910f7148b  controlfreec_annotated_cn_wxs_x_and_y_unresolved.tsv.gz
96f8e8e825639576130f86832bedde2c  controlfreec_annotated_cn_x_and_y.tsv.gz
c1246c0342e99f5679dbac11c05b5e7f  controlfreec_annotated_cn_x_and_y_unresolved.tsv.gz
6cf6efc6e5d8438f6dd0dfdb4243d4d7  freec-tumor-only_annotated_cn_autosomes.tsv.gz
c865c85e814f7b625bb3700f4490d466  freec-tumor-only_annotated_cn_autosomes_unresolved.tsv.gz
61da2895310a840df4efe6c0ef635247  freec-tumor-only_annotated_cn_x_and_y.tsv.gz
af327d67a6b069bcf511bc8a4cba33b2  freec-tumor-only_annotated_cn_x_and_y_unresolved.tsv.gz

[rjcorb]

LGTM! Reproduced all output as expected.