Updated README

GallVp · Jul 2, 2024 · f829ed1 · f829ed1
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -23,7 +23,7 @@ nf_core_version: 2.14.2.dev0
 repository_type: pipeline
 template:
   author: Usman Rashid
-  description: A pipeline to preprocess raw NGS data for downstream reuse across various
+  description: A pipeline to pre-process raw NGS data for downstream reuse across various
     pipelines
   force: true
   is_nfcore: false

diff --git a/README.md b/README.md
@@ -12,14 +12,34 @@
 
 **gallvp/prepngs** is a bioinformatics pipeline that pre-processes NGS data for downstream reuse across various pipelines.
 
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+```mermaid
+%%{init: {
+    'theme': 'base',
+    'themeVariables': {
+    'fontSize': '52px",
+    'primaryColor': '#9A6421',
+    'primaryTextColor': '#ffffff',
+    'primaryBorderColor': '#9A6421',
+    'lineColor': '#B180A8',
+    'secondaryColor': '#455C58',
+    'tertiaryColor': '#ffffff'
+  }
+}}%%
+flowchart LR
+  samplesheet(samplesheet.csv) ==> BAM2FASTQ
+  samplesheet(samplesheet.csv) ==> FASTQC
+
+  BAM2FASTQ ==> FASTQC
+  FASTQC ==> FASTP
+  FASTP ==> FASTQC2[FASTQC]
+  FASTQC2 ==> MULTIQC
+```
 
-1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Adapter trimming ([`FASTP`](https://github.com/OpenGene/fastp))
-3. Trimmed read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-4. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+1. BAM to FASTQ ([`PBTK`](https://github.com/PacificBiosciences/pbtk)), `optional`
+2. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+3. Adapter trimming ([`FASTP`](https://github.com/OpenGene/fastp))
+4. Trimmed read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
@@ -31,16 +51,15 @@ First, prepare a samplesheet with your input data that looks as follows:
 `samplesheet.csv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+sample,reads_1,reads_2
+test1,SRR4292758_00_R1.fastq.gz,SRR4292758_00_R2.fastq.gz
+test2,alz.ccs.bam
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
+Each row represents a fastq/bam file (single-end) or a pair of fastq files (paired end).
 
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run gallvp/prepngs \
    -profile <docker/singularity/.../institute> \
@@ -55,9 +74,21 @@ nextflow run gallvp/prepngs \
 
 gallvp/prepngs was originally written by Usman Rashid.
 
-We thank the following people for their extensive assistance in the development of this pipeline:
-
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+The pipeline uses nf-core modules contributed by following authors:
+
+<a href="https://github.com/drpatelh"><img src="https://github.com/drpatelh.png" width="50" height="50"></a>
+<a href="https://github.com/adamrtalbot"><img src="https://github.com/adamrtalbot.png" width="50" height="50"></a>
+<a href="https://github.com/grst"><img src="https://github.com/grst.png" width="50" height="50"></a>
+<a href="https://github.com/gallvp"><img src="https://github.com/gallvp.png" width="50" height="50"></a>
+<a href="https://github.com/maxulysse"><img src="https://github.com/maxulysse.png" width="50" height="50"></a>
+<a href="https://github.com/robsyme"><img src="https://github.com/robsyme.png" width="50" height="50"></a>
+<a href="https://github.com/mbeavitt"><img src="https://github.com/mbeavitt.png" width="50" height="50"></a>
+<a href="https://github.com/kevinmenden"><img src="https://github.com/kevinmenden.png" width="50" height="50"></a>
+<a href="https://github.com/jfy133"><img src="https://github.com/jfy133.png" width="50" height="50"></a>
+<a href="https://github.com/felixkrueger"><img src="https://github.com/felixkrueger.png" width="50" height="50"></a>
+<a href="https://github.com/ewels"><img src="https://github.com/ewels.png" width="50" height="50"></a>
+<a href="https://github.com/bunop"><img src="https://github.com/bunop.png" width="50" height="50"></a>
+<a href="https://github.com/abhi18av"><img src="https://github.com/abhi18av.png" width="50" height="50"></a>
 
 ## Contributions and Support
 

diff --git a/docs/contributors.sh b/docs/contributors.sh
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+module_authors=$(find ./modules -name meta.yml | xargs -I {} grep -A20 'authors:' {} | grep '\- ' | tr -d '"' | tr '[:upper:]' '[:lower:]' | awk '{print $2}')
+workflow_authors=$(find ./subworkflows -name meta.yml | xargs -I {} grep -A20 'authors:' {} | grep '\- ' | tr -d '"' | tr '[:upper:]' '[:lower:]' | awk '{print $2}')
+echo -e "${module_authors}\n${workflow_authors}" | sort -V | uniq -c | sort -k1,1 -r | awk '{print $2}' | sed -n 's|@\(.*\)|<a href="https://github.com/\1"><img src="https://github.com/\1.png" width="50" height="50"></a>|p'
diff --git a/modules.json b/modules.json
@@ -2,12 +2,12 @@
     "name": "gallvp/prepngs",
     "homePage": "https://github.com/gallvp/prepngs",
     "repos": {
-        "https://github.com/PlantandFoodResearch/nxf-modules.git": {
+        "https://github.com/GallVp/nxf-components.git": {
             "modules": {
-                "pfr": {
+                "gallvp": {
                     "pbtk/pbindex": {
                         "branch": "main",
-                        "git_sha": "429f064fb5fdf155405dda82a0334b8172f360e8",
+                        "git_sha": "b1b21af9d0298a87a328c3e5664eea7904538cfb",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/pfr/pbtk/pbindex/environment.yml → modules/gallvp/pbtk/pbindex/environment.yml b/modules/pfr/pbtk/pbindex/environment.yml → modules/gallvp/pbtk/pbindex/environment.yml
diff --git a/modules/pfr/pbtk/pbindex/main.nf → modules/gallvp/pbtk/pbindex/main.nf b/modules/pfr/pbtk/pbindex/main.nf → modules/gallvp/pbtk/pbindex/main.nf
diff --git a/modules/pfr/pbtk/pbindex/meta.yml → modules/gallvp/pbtk/pbindex/meta.yml b/modules/pfr/pbtk/pbindex/meta.yml → modules/gallvp/pbtk/pbindex/meta.yml
diff --git a/modules/pfr/pbtk/pbindex/tests/main.nf.test → ...es/gallvp/pbtk/pbindex/tests/main.nf.test b/modules/pfr/pbtk/pbindex/tests/main.nf.test → ...es/gallvp/pbtk/pbindex/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "PBTK_PBINDEX"
 
     tag "modules"
-    tag "modules_pfr"
+    tag "modules_gallvp"
     tag "pbtk"
     tag "pbtk/pbindex"
 

diff --git a/.../pfr/pbtk/pbindex/tests/main.nf.test.snap → ...llvp/pbtk/pbindex/tests/main.nf.test.snap b/.../pfr/pbtk/pbindex/tests/main.nf.test.snap → ...llvp/pbtk/pbindex/tests/main.nf.test.snap
diff --git a/modules/pfr/pbtk/pbindex/tests/tags.yml b/modules/pfr/pbtk/pbindex/tests/tags.yml
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -2,7 +2,7 @@
     "$schema": "http://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/gallvp/prepngs/master/nextflow_schema.json",
     "title": "gallvp/prepngs pipeline parameters",
-    "description": "A pipeline to preprocess raw NGS data for downstream reuse across various pipelines",
+    "description": "A pipeline to pre-process raw NGS data for downstream reuse across various pipelines",
     "type": "object",
     "definitions": {
         "input_output_options": {

diff --git a/workflows/prepngs.nf b/workflows/prepngs.nf
@@ -5,7 +5,7 @@
 */
 include { paramsSummaryMap                  } from 'plugin/nf-validation'
 
-include { PBTK_PBINDEX                      } from '../modules/pfr/pbtk/pbindex/main'
+include { PBTK_PBINDEX                      } from '../modules/gallvp/pbtk/pbindex/main'
 include { PBTK_BAM2FASTQ                    } from '../modules/nf-core/pbtk/bam2fastq/main'
 include { MULTIQC                           } from '../modules/nf-core/multiqc/main'