From adfda0f104d09fd1234c52b559083068e0bf5abf Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Fri, 10 May 2024 13:27:42 +0000
Subject: [PATCH] continue documentation

---
 docs/usage.md         | 22 +++++++++++++---------
 nextflow.config       |  1 -
 nextflow_schema.json  |  4 ----
 workflows/scrnaseq.nf |  3 +--
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/docs/usage.md b/docs/usage.md
index 2c1cd8d2..e5682b07 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -260,16 +260,20 @@ PBMC_10K_CMV,https://raw.githubusercontent.com/nf-core/test-datasets/modules/dat
 
 #### Additional supporting files
 
-Cellranger-arc needs a reference index directory that you can provide with `--cellranger_index`. Be aware, you can use
-for cellranger-arc the same index you use for cellranger ([see](https://kb.10xgenomics.com/hc/en-us/articles/4408281606797-Are-the-references-interchangeable-between-pipelines)).
-Yet, a cellranger-arc index might include additional data (e.g., TF binding motifs). Therefore, please first check if
-you have to create a new cellranger-arc index ([see here](https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references) for
-more information)
+Cellranger multi needs a reference for GEX and VDJ analysis. They are calculated on the fly given the reference files (`--fasta` and `--gtf`) provided, but users can also provide their own with: `--cellranger_index` and `--cellranger_vdj_index`, for GEX and VDJ, respectively.
 
-If you decide to create a cellranger-arc index, then you need to create a config file to generate the index. The pipeline
-can do this autmatically for you if you provide a `--fasta`, `--gtf`, and an optional `--motif` file. However, you can
-also decide to provide your own config file with `--cellrangerarc_config`, then you also have to specify with `--cellrangerarc_reference`
-the reference genome name that you have used and stated as _genome:_ in your config file.
+> When running cellranger multi, without any VDJ data, users can also skip VDJ automated ref building with: `--skip_cellrangermulti_vdjref`.
+
+Cellranger multi also requires some additional data/information when utilizing some specific Feature Barcode Technologies:
+
+TODO: talk about these:
+gex_frna_probe_set = null
+gex_target_panel = null
+gex_cmo_set = null
+fb_reference = null
+vdj_inner_enrichment_primers = null
+gex_barcode_sample_assignment = null
+cellranger_multi_barcodes = null
 
 ## Running the pipeline
 
diff --git a/nextflow.config b/nextflow.config
index 28bb69c9..3ea35e06 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -55,7 +55,6 @@ params {
     skip_emptydrops = false
 
     // CellrangerMulti parameters
-    cellranger_gex_index = null
     cellranger_vdj_index = null
     skip_cellrangermulti_vdjref = false // skip mkvdjref if not using VDJ data in cellranger/multi samplesheet
     gex_frna_probe_set   = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 469c6ade..14ecaf9d 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -313,10 +313,6 @@
             "description": "",
             "default": "",
             "properties": {
-                "cellranger_gex_index": {
-                    "type": "string",
-                    "description": "Specify a pre-built cellranger index for GEX analysis"
-                },
                 "cellranger_vdj_index": {
                     "type": "string",
                     "description": "Specify a pre-built cellranger index for VDJ analysis"
diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
index 4d36529f..1c419514 100644
--- a/workflows/scrnaseq.nf
+++ b/workflows/scrnaseq.nf
@@ -77,7 +77,6 @@ workflow SCRNASEQ {
     ch_universc_index = params.universc_index ? file(params.universc_index) : []
 
     //cellrangermulti params
-    cellranger_gex_index              = params.cellranger_gex_index      ? file(params.cellranger_gex_index, checkIfExists: true)      : []
     cellranger_vdj_index              = params.cellranger_vdj_index      ? file(params.cellranger_vdj_index, checkIfExists: true)      : []
     ch_multi_samplesheet              = params.cellranger_multi_barcodes ? file(params.cellranger_multi_barcodes, checkIfExists: true) : []
     empty_file                        = file("$projectDir/assets/EMPTY", checkIfExists: true)
@@ -273,7 +272,7 @@ workflow SCRNASEQ {
             ch_genome_fasta,
             ch_filter_gtf,
             ch_cellrangermulti_collected_channel,
-            cellranger_gex_index,
+            ch_cellranger_index,
             cellranger_vdj_index,
             ch_multi_samplesheet
         )