Enhancement/agfusion expansion #138
Conversation
pintoa1-mskcc
requested review from
anoronh4,
carynhale and
huyu335
and removed request for
huyu335
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can you add more description to either the top comment or a new comment, explaining in further detail what you're addressing? That way it's easier to look back through the history and figure it out. |
| @@ -10,7 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | |||
| - [#117](https://github.com/mskcc/forte/pull/117) - add supporting-reads_gene-fusions\*.zip files to fusioncatcher outputs | |||
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| - [#118](https://github.com/mskcc/forte/pull/118) - change the way the plug-n-play starfusion reference is downloaded. | |||
| - [#126](https://github.com/mskcc/forte/pull/126) - enable clinical genes prioritization in Metafusion | |||
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| - [#126](https://github.com/mskcc/forte/pull/126) - enable transcript prioritization in Metafusion | |||
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Add a new line for this PR 138
| @@ -15,7 +15,7 @@ RT_call_filter=1 | |||
| blck_filter=1 | |||
| ANC_filter=1 | |||
| usage() { | |||
| echo "Usage: Metafusion_forte.sh --num_tools=<minNumToolsCalled> --genome_fasta <FASTA adds SEQ to fusion> --recurrent_bedpe <blacklistFusions> --outdir <outputDirectory> --cff <cffFile> --gene_bed <geneBedFile> --gene_info <geneInfoFile> --clinical_genes <clinicalGenes>" 1>&2; | |||
| echo "Usage: Metafusion_forte.sh --num_tools=<minNumToolsCalled> --genome_fasta <FASTA adds SEQ to fusion> --recurrent_bedpe <blacklistFusions> --outdir <outputDirectory> --cff <cffFile> --gene_bed <geneBedFile> --gene_info <geneInfoFile> --clinical_genes <transcript_allowlist>" 1>&2; | |||
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should we also rename the parameter --clinical_genes to something like --allowed_transcripts?
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| usage <- function() { | ||
| message("Usage:") | ||
| message("add_flags_agfusion_clinical.R --cff-file <file.cff> --agfusion-file <agfusion.tsv> --transcript_allowlist <transcript_allowlist.txt> --out-prefix <prefix>") |
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seems like the parameters should actually be cff and agfusion, not cff-file and agfusion-file?
| by.x = "3'_transcript", | ||
| by.y = "ensembl_transcript", | ||
| all.x = T, | ||
| all.y = F) |
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we're not going to filter out agfusion results where one or both transcripts are not on the transcript allowlist? not saying this is wrong, just checking
| @@ -38,7 +38,7 @@ process METAFUSION_RUN { | |||
| --gene_info $info \\ | |||
| --genome_fasta $fasta \\ | |||
| --recurrent_bedpe $blocklist \\ | |||
| --clinical_genes $clinicalgenes \\ | |||
| --clinical_genes $transcript_allowlist \\ | |||
| @@ -129,7 +129,7 @@ workflow FORTE { | |||
| PREPROCESS_READS.out.reads_trimmed, | |||
| PREPROCESS_READS.out.reads_untrimmed, | |||
| PREPARE_REFERENCES.out.star_index, | |||
| PREPARE_REFERENCES.out.fasta, | |||
| PREPARE_REFERENCES.out.fasta, | |||
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| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'ghcr.io/rocker-org/devcontainer/tidyverse:4' : | ||
| 'ghcr.io/rocker-org/devcontainer/tidyverse:4' }" |
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change this to a more specific version to make sure that it is reproducible, i would suggest: ghcr.io/rocker-org/tidyverse:4.4.2
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).