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nf-core · Oct 5, 2023 · 4d7c502 · 4d7c502
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,4 +1,4 @@
 repository_type: pipeline
 
 lint:
-  template_strings: False # "Jinja string found in" bin/create_regex.py and bin/seurat_qc.R
+  template_strings: False # "Jinja string found in" bin/create_regex.py and bin/seurat_qc.R
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -19,7 +19,7 @@
   > You Y, Prawer Y D, De Paoli-Iseppi R, Hunt C P, Parish C L, Shim H, Clark M B. Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE. bioRxiv 2022 Aug .08.16.504056; doi: 10.1101/2022.08.16.504056.
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-  
+
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
 
 - [IsoQuant](https://pubmed.ncbi.nlm.nih.gov/36593406/)
@@ -87,6 +87,7 @@
   > Wickham H, Averick M, Bryan J, Winston C, McGowan LD, François R, Grolemund G, Hayes A , Henry L, Hester J, Kuhn M, Pedersen TL, Miller E, Bache SM, Müller K, Ooms J, Robinson D, Seidel DP, Spinu V, Takahashi K, Vaughan D, Wilke C, Woo K, Yutani H. Welcome to the Tidyverse. Journal of Open Source Software 2019, 4(43), 1686, doi:10.21105/joss.01686
 
 ## Python libraries
+
 - [Biopython](https://pubmed.ncbi.nlm.nih.gov/19304878/)
 
   > Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11):1422-3 doi:10.1093/bioinformatics/btp163. PubMed PMID: 19304878; PubMed Central PMCID: PMC2682512.

diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
 
 ## Introduction
 
-**nf-core/scnanoseq** is a bioinformatics best-practice analysis pipeline for 10X Genomics single-cell/nuclei RNA-seq for data derived from Oxford Nanopore Q20+ chemistry ([R10.4 flow cells (>Q20)](https://nanoporetech.com/about-us/news/oxford-nanopore-announces-technology-updates-nanopore-community-meeting)). Due to the expectation of >Q20 quality, the input data for the pipeline is not dependent on Illumina paired data. 
+**nf-core/scnanoseq** is a bioinformatics best-practice analysis pipeline for 10X Genomics single-cell/nuclei RNA-seq for data derived from Oxford Nanopore Q20+ chemistry ([R10.4 flow cells (>Q20)](https://nanoporetech.com/about-us/news/oxford-nanopore-announces-technology-updates-nanopore-community-meeting)). Due to the expectation of >Q20 quality, the input data for the pipeline is not dependent on Illumina paired data.
 
 <!-- TODO: after test write brief sentence on exon only vs intron method (1 and 2) --->
 
@@ -35,8 +35,8 @@ On release, automated continuous integration tests run the pipeline on a full-si
 5. Pre-extraction QC in the R2 reads ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [`NanoPlot`](https://github.com/wdecoster/NanoPlot))
 6. Barcode detection using a custom whitelist or 10X whitelist. [`BLAZE`](https://github.com/shimlab/BLAZE)
 7. Extract barcodes. Consists of the following steps:
-    1. Parse FASTQ files into R1 reads containing barcode and UMI and R2 reads containing sequencing without barcode and UMI (custom script `./bin/pre_extract_barcodes.py`)
-    2. Re-zip FASTQs ([`pigz`](https://github.com/madler/pigz))
+   1. Parse FASTQ files into R1 reads containing barcode and UMI and R2 reads containing sequencing without barcode and UMI (custom script `./bin/pre_extract_barcodes.py`)
+   2. Re-zip FASTQs ([`pigz`](https://github.com/madler/pigz))
 8. Post-extraction QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [`NanoPlot`](https://github.com/wdecoster/NanoPlot))
 9. Alignment ([`minimap2`](https://github.com/lh3/minimap2))
 10. SAMtools processing including ([`SAMtools`](http://www.htslib.org/doc/samtools.html)):
@@ -74,9 +74,9 @@ Each row represents a fastq file (single-end) or a pair of fastq files (paired e
 
 -->
 
-   ```console
-   nextflow run nf-core/scnanoseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
-   ```
+```console
+nextflow run nf-core/scnanoseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+```
 
 ```bash
 nextflow run nf-core/scnanoseq \
@@ -106,8 +106,8 @@ We thank the following people for their extensive assistance in the development
 
 We would also like to thank the following people and groups for their support, including financial support:
 
-* Dr. Elizabeth Worthey
-* University of Alabama at Birmingham Biological Data Science Core (U-BDS), RRID:SCR_021766, https://github.com/U-BDS
+- Dr. Elizabeth Worthey
+- University of Alabama at Birmingham Biological Data Science Core (U-BDS), RRID:SCR_021766, https://github.com/U-BDS
 
 <!-- TODO from Lara: check that all financial support has been stated -->
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -4,90 +4,88 @@ report_comment: >
   <a href="https://nf-co.re/scnanoseq/0.1.0dev/output" target="_blank">documentation</a>.
 
 report_section_order:
-    "nf-core-scnanoseq-methods-description":
-      order: -1000
-    software_versions:
-      order: -1001
-    "nf-core-scnanoseq-summary":
-        order: -1002
-    fastqc_postextract_fastqc_per_base_sequence_quality: remove
-    fastqc_postextract_fastqc_per_sequence_quality_scores: remove
-    fastqc_postextract_fastqc_per_base_sequence_content: remove
-    fastqc_postextract_fastqc_per_sequence_gc_content: remove
-    fastqc_postextract_fastqc_per_base_n_content: remove
-    fastqc_postextract_fastqc_sequence_length_distribution: remove
-    fastqc_postextract_fastqc_sequence_duplication_levels: remove
-    fastqc_postextract_fastqc_overrepresented_sequences: remove
-    fastqc_postextract_fastqc_adapter_content: remove
-    fastqc_postextract_fastqc_status_checks: remove
+  "nf-core-scnanoseq-methods-description":
+    order: -1000
+  software_versions:
+    order: -1001
+  "nf-core-scnanoseq-summary":
+    order: -1002
+  fastqc_postextract_fastqc_per_base_sequence_quality: remove
+  fastqc_postextract_fastqc_per_sequence_quality_scores: remove
+  fastqc_postextract_fastqc_per_base_sequence_content: remove
+  fastqc_postextract_fastqc_per_sequence_gc_content: remove
+  fastqc_postextract_fastqc_per_base_n_content: remove
+  fastqc_postextract_fastqc_sequence_length_distribution: remove
+  fastqc_postextract_fastqc_sequence_duplication_levels: remove
+  fastqc_postextract_fastqc_overrepresented_sequences: remove
+  fastqc_postextract_fastqc_adapter_content: remove
+  fastqc_postextract_fastqc_status_checks: remove
 
 export_plots: true
 
 top_modules:
-    - general_stats
-    - custom_content
-    - samtools
-    - fastqc:
-        name: "FastQC (raw)"
-        anchor: "fastqc"
-        info: "This section of the report shows FastQC results of the raw data"
-        path_filters:
-            - "*raw*fastqc*"
-    - fastqc:
-        name: "FastQC (post trimmed)"
-        anchor: "fastqc_posttrim"
-        info: "This section of the report shows FastQC results of the trimmed 
-               data"
-        path_filters:
-            - "*trimmed*fastqc*"
-    - fastqc:
-        name: "FastQC (post extract)"
-        anchor: "fastqc_postextract"
-        info: "This section of the report shows FastQC results of the trimmed 
-               and umi extracted data"
-        path_filters:
-            - "*extracted*fastqc*"
+  - general_stats
+  - custom_content
+  - samtools
+  - fastqc:
+      name: "FastQC (raw)"
+      anchor: "fastqc"
+      info: "This section of the report shows FastQC results of the raw data"
+      path_filters:
+        - "*raw*fastqc*"
+  - fastqc:
+      name: "FastQC (post trimmed)"
+      anchor: "fastqc_posttrim"
+      info: "This section of the report shows FastQC results of the trimmed
+        data"
+      path_filters:
+        - "*trimmed*fastqc*"
+  - fastqc:
+      name: "FastQC (post extract)"
+      anchor: "fastqc_postextract"
+      info: "This section of the report shows FastQC results of the trimmed
+        and umi extracted data"
+      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)"
+  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
-        order:
-        - transcript_seurat_stats_module
-        - gene_seurat_stats_module
+  seurat_section:
+    parent_id: seurat_section
+    order:
+      - transcript_seurat_stats_module
+      - gene_seurat_stats_module
 
 custom_data:
+  gene_seurat_stats_module:
+    parent_id: seurat_section
+    parent_name: "Seurat Section"
+    parent_description: "Preliminary expression analysis summary completed with
+      Seurat. Note that these numbers are generated
+      without any filtering done on the dataset"
+    section_name: "Gene Seurat Stats"
+    file_format: "tsv"
+    plot_type: "table"
 
-    gene_seurat_stats_module:
-        parent_id: seurat_section
-        parent_name: "Seurat Section"
-        parent_description: "Preliminary expression analysis summary completed with
-                            Seurat. Note that these numbers are generated
-                            without any filtering done on the dataset"
-        section_name: "Gene Seurat Stats"
-        file_format: "tsv"
-        plot_type: "table"
-
-    transcript_seurat_stats_module:
-        parent_id: seurat_section
-        parent_name: "Seurat Section"
-        parent_description: "Preliminary expression analysis summary completed with
-                            Seurat. Note that these numbers are generated
-                            without any filtering done on the dataset"
-        section_name: "Transcript Seurat Stats"
-        file_format: "tsv"
-        plot_type: "table"
+  transcript_seurat_stats_module:
+    parent_id: seurat_section
+    parent_name: "Seurat Section"
+    parent_description: "Preliminary expression analysis summary completed with
+      Seurat. Note that these numbers are generated
+      without any filtering done on the dataset"
+    section_name: "Transcript Seurat Stats"
+    file_format: "tsv"
+    plot_type: "table"
 
 sp:
-    gene_seurat_stats_module:
-        fn: "gene.*.tsv"
-    transcript_seurat_stats_module:
-        fn: "transcript.*.tsv"
-
+  gene_seurat_stats_module:
+    fn: "gene.*.tsv"
+  transcript_seurat_stats_module:
+    fn: "transcript.*.tsv"