cleaning up multiqc config, sample samplesheet and output.md

assets/multiqc_config.yml

@@ -52,14 +52,6 @@ top_modules:
       path_filters:
         - "*extracted*fastqc*"
 
-section_comments:
-  fastqc_posttrim: "Please note that if 'prowler' is selected as the trimming
-    method, these qc's should be looked at closely. Prowler does not
-    always remove reads, as it will replace low quality windows with
-    N's, which can have notable effects on the qc's below. For more
-    information on the prowler algorithm, please refer to the
-    [Prowler paper](https://doi.org/10.1093/bioinformatics/btab630)"
-
 custom_content:
   seurat_section:
     parent_id: seurat_section

assets/samplesheet.csv

@@ -1,3 +1,4 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,fastq,cell_count
+ERR9958133,/path/to/fastq/files/ERR9958133.fastq.gz,1000
+ERR9958134,/path/to/fastq/files/ERR9958134.fastq.gz,1000
+ERR9958135,/path/to/fastq/files/ERR9958135.fastq.gz,1000

docs/output.md

@@ -6,8 +6,6 @@ This document describes the output produced by the pipeline. Most of the plots a
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-<!-- TODO nf-core: Write this documentation describing your workflow's output -->
-
 ## Pipeline overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
@@ -23,7 +21,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - [Barcode Correction](#barcode-correction) - Barcode whitelist correction
   - [UMI Deduplication](#umi-deduplication) - UMI-based deduplication
 - [Feature-Barcode Quantification](#feature-barcode-quantification)
-  - [IsoQuant](#isoquant) - Feature-barcode quantification
+  - [IsoQuant](#isoquant) - Feature-barcode quantification (gene and transcript level)
   - [Seurat](#seurat) - Feature-barcode matrix QC
 - [Quality Control](#quality-control)
   - [FastQC](#fastqc) - Fastq QC
@@ -143,7 +141,7 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 
 ![MultiQC - umitools dedup](images/umitools_dedup.png)
 
-[UMI-Tools](https://umi-tools.readthedocs.io/en/latest/reference/dedup.html) deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. The identification of duplicate reads is performed in an error-aware manner by building networks of related UMIs 
+[UMI-Tools](https://umi-tools.readthedocs.io/en/latest/reference/dedup.html) deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. The identification of duplicate reads is performed in an error-aware manner by building networks of related UMIs
 
 ## Feature-Barcode Quantification
 ### IsoQuant
@@ -175,7 +173,7 @@ Barcode correction is a custom script that uses the whitelist generated by BLAZE
 
 ![MultiQC - seurat](images/seurat.png)
 
-[Seurat](https://satijalab.org/seurat/) is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. 
+[Seurat](https://satijalab.org/seurat/) is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
 
 ## Quality Control
 ### FastQC