🐛 Fix Collapse bug

[migbro]

🔧 fixed collapse bug

Purpose/implementation Section

What scientific question is your analysis addressing?

A bug fix in collapse gene logic, and issues with package availability in docker pull

What was your approach?

Look at the code, identify the cause

What GitHub issue does your pull request address?

The return for the function was happening inside loop, instead of returning after the loop completed, resulting on in only one duplicate gene being collapsed and all others being dropped. Also changes one of the step to pull from annoFuse docker instead of tidyverse to make required optparse package readily available

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

Which areas should receive a particularly close look?

Updates to python script and results from https://cavatica.sbgenomics.com/u/d3b-bixu-ops/open-target-tcga-rnaseq-counts/tasks/6f6651b8-850d-4cfc-96fe-467f1b4b455a/

Is there anything that you want to discuss further?

Address #550 #552 #551

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

Results

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

Outputs from https://cavatica.sbgenomics.com/u/d3b-bixu-ops/open-target-tcga-rnaseq-counts/tasks/6f6651b8-850d-4cfc-96fe-467f1b4b455a/

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]

looks good to me

> tcga_take2 %>%
+   filter(grepl("CYB561D2", gene_name)) %>%
+   select(gene_name, `TCGA-02-0047-01A-01R-1849-01`, `TCGA-02-0055-01A-01R-1849-01`)
# A tibble: 1 × 3
  gene_name `TCGA-02-0047-01A-01R-1849-01` `TCGA-02-0055-01A-01R-1849-01`
  <chr>                              <dbl>                          <dbl>
1 CYB561D2                             522                            687
> tcga_take2 %>%
+   filter(grepl("CD99", gene_name)) %>%
+   select(gene_name, `TCGA-02-0047-01A-01R-1849-01`, `TCGA-02-0055-01A-01R-1849-01`)
# A tibble: 3 × 3
  gene_name `TCGA-02-0047-01A-01R-1849-01` `TCGA-02-0055-01A-01R-1849-01`
  <chr>                              <dbl>                          <dbl>
1 CD99L2                              6159                           5116
2 CD99P1                                96                            317
3 CD99                               23661                          36155
> tcga_counts_not_collapsed <- read_tsv("~/Downloads/TCGA-gene-expression-gene-count.liftover (1).tsv.gz")
Rows: 60660 Columns: 11125                                                                                                 
── Column specification ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr     (2): gene_id, gene_name
dbl (11123): TCGA-02-0047-01A-01R-1849-01, TCGA-02-0055-01A-01R-1849-01, TCGA-02-2483-01A-01R-1849-01, TCGA-02-2485-01A-01R-1849-01, TC...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
> tcga_counts_not_collapsed %>%
+   filter(grepl("CD99", gene_name)) %>%
+   select(gene_name, `TCGA-02-0047-01A-01R-1849-01`, `TCGA-02-0055-01A-01R-1849-01`)
# A tibble: 5 × 3
  gene_name `TCGA-02-0047-01A-01R-1849-01` `TCGA-02-0055-01A-01R-1849-01`
  <chr>                              <dbl>                          <dbl>
1 CD99L2                              6159                           5116
2 CD99P1                                 0                              0
3 CD99                                   0                              0
4 CD99P1                                96                            317
5 CD99                               23661                          36155

[jharenza]

Merging this since this is not run in GA