Update run fragpipe script to take command line args by rjcorb · Pull Request #25 · rokitalab/fragpipe

rjcorb · 2025-10-09T20:27:18Z

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR updates run_fragpipe.sh as follows:

now requires command line arguments for: 1) query fasta file, 2) manifest file, 3) workflow file, and 4) results directory path
Add optional argument --cohort that takes values "cptac" or "hope". If specified, the script will attempt to mount associated cavatica project and copy and unzip mzML files. This can also be run with argument --run_subset to only run the first experiment of each cohort dataset.
adds step to run blast filtering against canonical uniprot peptides.

What was your approach?

What GitHub issue does your pull request address?

#24

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?

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)?

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.

Documentation Checklist

This analysis module has a README and it is up to date.
The analytical code is documented and contains comments.

rjcorb · 2025-10-09T20:28:13Z

I would like to add additional scripts here (or perhaps conditionals within the current shell script) to process HOPE and CPTAC mzML files when querying these cohorts. This will likely require an additional --cohort argument.

… filtering

chaodi51 · 2025-12-01T19:22:33Z

@rjcorb It seems Blast is not installed in the Docker:

bash run_fragpipe.sh --query input/custom.fasta --manifest input/PDC000180filesmanifest.fp-manifest --workflow input/PDC000180customworkflow.workflow --res_dir ./test --cohort hope  
Filtering out 100% matches to canonical peptides...
scripts/run_blast_filter.sh: line 36: blastp: command not found

rjcorb · 2025-12-04T20:47:01Z

@chaodi51 I have removed the blast filter step so I think this should be good to test now. Can you run the following two test run scripts from root to check if the runs complete?

--query input/custom.fasta \
--manifest input/PDC000180filesmanifest.fp-manifest \
--workflow input/PDC000180customworkflow.workflow \
--res_dir results \
--cohort "cptac" \
--run_subset

bash run_fragpipe.sh \
--query input/custom.fasta \
--manifest input/HOPE-files-manifest.fp-manifest \
--workflow input/HOPEproteome_TMT11workflow.workflow \
--res_dir results \
--cohort "hope" \
--run_subset

chaodi51 · 2025-12-11T21:00:16Z

It seems the Dockerfile is installing fragPipe-23.1, but the docker image is still fragPipe-22.0 in the registry and the shell script is using fragPipe-22.0. Can you make these consistent? @rjcorb

rjcorb · 2025-12-12T15:03:59Z

@chaodi51 the Dockerfile has been updated and I think the issue with running the HOPE cohort should also be resolved.

chaodi51 · 2025-12-12T21:58:25Z

@chaodi51 the Dockerfile has been updated and I think the issue with running the HOPE cohort should also be resolved.

The script is working now. Could you also take a look at my comments in the script? I don’t quite understand the part about removing canonical peptides. Thanks! @rjcorb

chaodi51 · 2025-12-11T20:49:52Z

run_fragpipe.sh

-mv *decoys-contam-custom.fasta.fas decoys-contam-custom-canonical.fasta
+gunzip -c $Uniprot_canonical | $tools_dir/Philosopher/philosopher-v5.1.1 database --custom $query_fullpath --add /dev/stdin --contam
+
+# Remove canonical peptides annotated to genes in custom fasta


Why not remove canonical peptides in the custom.fasta at the first place and then build the database?

chaodi51 · 2025-12-11T21:46:26Z

run_fragpipe.sh

+             if (index($0,g)) {keep=0; break}
+         }
+     }
+     keep' *decoys-contam-custom.fasta.fas > decoys-contam-custom-canonical.fasta


This awk command seems did not filter anything. I got a 2025-12-11-decoys-contam-custom.fasta.fas file from last step and as input here, which is the same as decoys-contam-custom-canonical.fasta

I'm a bit confused about this. The gene_symbols.txt file contains:

GN=chr8 GN=chr9 GN=chrX GN=chrY GN=fusion|ADCYAP1--LINC01904(23137),ENSG00000272461(11462)|ADCYAP1|chr18 GN=fusion|ANK2--PTCH1|ANK2|chr4 GN=fusion|CMTM1--CMTM1|CMTM1|chr16 GN=fusion|CREBBP--EP400|CREBBP|chr16

However, the combined FASTA file decoys-contam-custom.fasta.fas would never contain peptide headers matching the patterns GN=chr or GN=fusion*, since the original source files (UP000005640_9606.fasta.gz and customa.fasta) do not include those annotations.

@chaodi51 I just updated the gene filtering. I think this may have been applicable in a different case previously, but I agree, this was not functioning as expected using the original code. I think, with the updates, you should see several hundred genes filtered out of the decoys-contam-custom-canonical.fasta file.

@rjcorb Now I have an error:

bash run_fragpipe.sh --query input/custom_filtered.fasta --manifest input/PDC000180filesmanifest.fp-manifest --workflow input/PDC000180customworkflow.workflow --res_dir results --cohort "cptac" --run_subset Adding decoys and contaminants to FASTA files.. time="21:49:47" level=info msg="Executing Workspace v5.1.1" time="21:49:47" level=info msg="Creating workspace" time="21:49:47" level=warning msg="A meta data folder was found and will not be overwritten. " time="21:49:47" level=info msg=Done time="21:49:47" level=info msg="Executing Database v5.1.1" time="21:49:47" level=info msg="Generating the target-decoy database" time="21:49:48" level=info msg="Creating file" time="21:49:48" level=info msg=Done awk: line 1: syntax error at or near ,

ah I think it's an issue with running awk within the docker container. I have fixed the issue.

awk: cannot open *decoys-contam-custom.fasta.fas (No such file or directory)
You may also need to change *decoys-contam-custom.fasta.fas to *decoys-contam-custom_filtered.fasta.fas since we're now using custom_filtered.fasta instead of custom.fasta from Impact-trail runs? @rjcorb

chaodi51 · 2025-12-17T23:53:19Z

run_fragpipe.sh

+  print line
+}' "$query_fullpath" \
+| grep -v '^$' \
+| sort -u > splice_event_genes.txt


chaodi51 · 2026-02-05T14:45:53Z

These issues have been resolved in the fragpipe_cwl workflow, you can close it.

rjcorb added 2 commits October 9, 2025 16:22

add command line args to shell script

687703e

add uniprot ref files

aa198f6

rjcorb added the work in progress label Oct 9, 2025

add functionality to support cptac,hope dataset queries; update blast…

2e977b8

… filtering

This was referenced Oct 10, 2025

Fragpipe CPTAC run for tumor-enriched splice event-derived peptides #21

Closed

Workflow for running fragpipe on impact trial test data #23

Closed

jharenza assigned rjcorb Oct 13, 2025

rjcorb added ready for review and removed work in progress labels Oct 23, 2025

jharenza requested a review from chaodi51 November 19, 2025 15:14

rjcorb added 3 commits December 4, 2025 15:34

rm blast filter step, add sbfs mount checks

c525173

rm uniprot files

fe37630

update mount checks to be compatible with HOPE

65bd484

rjcorb added 3 commits December 12, 2025 09:55

update fasta path in HOPE workflow file

9ea6140

revert Dockerfile to Fragpipe v22.0

7cdd593

Merge branch 'main' into rjcorb/24-command-line-args

8ed9055

chaodi51 reviewed Dec 16, 2025

View reviewed changes

rjcorb added 2 commits December 16, 2025 14:42

update gene filtering from custom + canonical fasta

f7cb98f

update splice event gene filtering

7ad4e22

chaodi51 reviewed Dec 17, 2025

View reviewed changes

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Purpose/implementation Section

What scientific question is your analysis addressing?

What was your approach?

What GitHub issue does your pull request address?

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?

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)?

What is your summary of the results?

Reproducibility Checklist

Documentation Checklist

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rjcorb commented Oct 9, 2025 •

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