From 079bb7ec7a7dd5f4a2009463106e785fabbdd178 Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Wed, 30 Oct 2024 11:15:13 +0000
Subject: [PATCH] added small comment to local modules

---
 modules/local/adata_barcodes.nf                    | 6 ++++++
 modules/local/alevinqc.nf                          | 5 +++++
 modules/local/anndatar_convert.nf                  | 5 +++++
 modules/local/concat_h5ad.nf                       | 6 ++++++
 modules/local/gffread_transcriptome.nf             | 5 +++++
 modules/local/gtf_gene_filter.nf                   | 5 +++++
 modules/local/mtx_to_h5ad.nf                       | 5 +++++
 modules/local/parse_cellrangermulti_samplesheet.nf | 5 +++++
 modules/local/simpleaf_index.nf                    | 5 +++++
 modules/local/simpleaf_quant.nf                    | 5 +++++
 modules/local/star_align.nf                        | 5 +++++
 11 files changed, 57 insertions(+)

diff --git a/modules/local/adata_barcodes.nf b/modules/local/adata_barcodes.nf
index 2aef8ec9..630d90ae 100644
--- a/modules/local/adata_barcodes.nf
+++ b/modules/local/adata_barcodes.nf
@@ -1,4 +1,10 @@
 process ADATA_BARCODES {
+
+    //
+    // Module from nf-core/scdownstream.
+    // This module performs the subset of the h5ad file to only contain barcodes that passed emptydrops filter with cellbender
+    //
+
     tag "$meta.id"
     label 'process_single'
 
diff --git a/modules/local/alevinqc.nf b/modules/local/alevinqc.nf
index 9000d79e..777a1371 100644
--- a/modules/local/alevinqc.nf
+++ b/modules/local/alevinqc.nf
@@ -1,4 +1,9 @@
 process ALEVINQC {
+
+    //
+    // This module executes alevinfry QC reporting tool on alevin results
+    //
+
     tag "$meta.id"
     label 'process_low'
 
diff --git a/modules/local/anndatar_convert.nf b/modules/local/anndatar_convert.nf
index 12a2b1b4..8e4c242e 100644
--- a/modules/local/anndatar_convert.nf
+++ b/modules/local/anndatar_convert.nf
@@ -1,4 +1,9 @@
 process ANNDATAR_CONVERT {
+
+    //
+    // This module uses the anndata R package to convert h5ad files in different formats
+    //
+
     tag "${meta.id}"
 
     label 'process_medium'
diff --git a/modules/local/concat_h5ad.nf b/modules/local/concat_h5ad.nf
index 393a7353..c875ba3c 100644
--- a/modules/local/concat_h5ad.nf
+++ b/modules/local/concat_h5ad.nf
@@ -1,4 +1,10 @@
 process CONCAT_H5AD {
+
+    //
+    // This module concatenates all h5ad, per type (raw, filtered, etc.) files generated during pipeline execution
+    //
+
+
     tag "${meta.id}"
 
     label 'process_medium'
diff --git a/modules/local/gffread_transcriptome.nf b/modules/local/gffread_transcriptome.nf
index ab573b07..671b6726 100644
--- a/modules/local/gffread_transcriptome.nf
+++ b/modules/local/gffread_transcriptome.nf
@@ -1,4 +1,9 @@
 process GFFREAD_TRANSCRIPTOME {
+
+    //
+    // This module uses gffread to filter input to generate a transcripts fasta
+    //
+
     tag "${genome_fasta}"
     label 'process_low'
 
diff --git a/modules/local/gtf_gene_filter.nf b/modules/local/gtf_gene_filter.nf
index 063bd228..10af352b 100644
--- a/modules/local/gtf_gene_filter.nf
+++ b/modules/local/gtf_gene_filter.nf
@@ -1,4 +1,9 @@
 process GTF_GENE_FILTER {
+
+    //
+    // This module executes a custom script to filter input gtf to contain only annotations present in input genome
+    //
+
     tag "$fasta"
     label 'process_low'
 
diff --git a/modules/local/mtx_to_h5ad.nf b/modules/local/mtx_to_h5ad.nf
index 27e1070a..f54318f1 100644
--- a/modules/local/mtx_to_h5ad.nf
+++ b/modules/local/mtx_to_h5ad.nf
@@ -1,4 +1,9 @@
 process MTX_TO_H5AD {
+
+    //
+    // This module executes different conversion template scripts (per aligner) for converting output mtx files into h5ad files
+    //
+
     tag "$meta.id"
     label 'process_medium'
 
diff --git a/modules/local/parse_cellrangermulti_samplesheet.nf b/modules/local/parse_cellrangermulti_samplesheet.nf
index df616995..e8f56b67 100644
--- a/modules/local/parse_cellrangermulti_samplesheet.nf
+++ b/modules/local/parse_cellrangermulti_samplesheet.nf
@@ -1,4 +1,9 @@
 process PARSE_CELLRANGERMULTI_SAMPLESHEET {
+
+    //
+    // This module contains a custom script for checking special cellranger multi samplesheet
+    //
+
     label 'process_low'
     publishDir = [ enabled: false ]
 
diff --git a/modules/local/simpleaf_index.nf b/modules/local/simpleaf_index.nf
index 8e8bd519..5c362c99 100644
--- a/modules/local/simpleaf_index.nf
+++ b/modules/local/simpleaf_index.nf
@@ -1,4 +1,9 @@
 process SIMPLEAF_INDEX {
+
+    //
+    // This module executes simpleaf to generate alevin genome index
+    //
+
     tag "$transcript_gtf"
     label "process_medium"
 
diff --git a/modules/local/simpleaf_quant.nf b/modules/local/simpleaf_quant.nf
index abb58404..9241b210 100644
--- a/modules/local/simpleaf_quant.nf
+++ b/modules/local/simpleaf_quant.nf
@@ -1,4 +1,9 @@
 process SIMPLEAF_QUANT {
+
+    //
+    // This module executes simpleaf to perform quantification with alevin
+    //
+
     tag "$meta.id"
     label 'process_high'
 
diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
index 4b3df1e1..70d6770c 100644
--- a/modules/local/star_align.nf
+++ b/modules/local/star_align.nf
@@ -1,4 +1,9 @@
 process STAR_ALIGN {
+
+    //
+    // This module executes STAR align quantification
+    //
+
     tag "$meta.id"
     label 'process_high'