correct issue with --help and reorganize things

.gitignore

@@ -3,8 +3,6 @@
 work
 .nextflow
 .nextflow.*
-tests/resources/output*
-tests/resources/input_files*
 venv
 __pycache__
 output

Makefile

@@ -12,6 +12,7 @@ clean:
 	rm -rf .nextflow*
 
 test:
+	nextflow main.nf --help
 	nextflow main.nf -profile test,conda --output output/test1
 	nextflow main.nf -profile test,conda --output output/test2 --filter PASS,MNV
 	nextflow main.nf -profile test,conda --output output/test3 --skip_decompose_complex

README.md

@@ -2,9 +2,9 @@
 
 [![DOI](https://zenodo.org/badge/372133189.svg)](https://zenodo.org/badge/latestdoi/372133189)
 
-This pipeline aims at normalizing variants represented in a VCF into the convened normal form as described in Tan et al., 2015. 
-The variant normalization is based on the implementation in vt and bcftools. 
-The pipeline is implemented on the Nextflow framework.
+This pipeline aims at normalizing variants represented in a VCF into the convened normal form as described in Tan 2015. 
+The variant normalization is based on the implementation in vt (Tan 2015) and bcftools (Danecek 2021). 
+The pipeline is implemented on the Nextflow (Di Tommaso 2017) framework.
 
 The pipeline consists of the following steps:
  * Variant filtering (optional)
@@ -18,7 +18,7 @@ The output consists of:
  * Summary statistics before and after normalization
 
 
-![Pipeline](variant_normalization_pipeline.png)
+![Pipeline](images/variant_normalization_pipeline.png)
 
 ## Examples
 
@@ -108,7 +108,7 @@ Same as MNVs this behaviour can de disabled with `--skip_decompose_complex`.
 ## How to run it
 
  ```
- $ nextflow run tron-bioinformatics/tron-variant-normalization -r v1.0.0 --help
+ $ nextflow run tron-bioinformatics/tronflow-variant-normalization --help
  
  TronFlow VCF normalization v${VERSION}
 

filter_passed.sh → bin/filter_passed.sh

@@ -1,5 +1,5 @@
-#!/usr/bin/env bash
-vcf=$1
-
-# keeps only the passed variants
-bcftools view --apply-filters PASS -o `basename $vcf .vcf`.passed.vcf $vcf
+#!/usr/bin/env bash
+vcf=$1
+
+# keeps only the passed variants
+bcftools view --apply-filters PASS -o `basename $vcf .vcf`.passed.vcf $vcf

summary.sh → bin/summary.sh

@@ -1,7 +1,7 @@
-#!/usr/bin/env bash
-vcf=$1
-
-module load anaconda/3/2019
-
-bcftools summary $vcf > `basename $vcf .vcf`.stats
-plot-vcfstats -p `basename $vcf .vcf`.stats_plots `basename $vcf .vcf`.stats
+#!/usr/bin/env bash
+vcf=$1
+
+module load anaconda/3/2019
+
+bcftools summary $vcf > `basename $vcf .vcf`.stats
+plot-vcfstats -p `basename $vcf .vcf`.stats_plots `basename $vcf .vcf`.stats

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: tronflow-variant-normalization-1.0.0
+name: tronflow-variant-normalization
 channels:
   - conda-forge
   - bioconda

main.nf

@@ -11,7 +11,7 @@ params.memory = "4g"
 
 
 if (params.help) {
-    log.info params.help
+    log.info params.help_message
     exit 0
 }
 

nextflow.config

@@ -27,7 +27,7 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-VERSION = '1.0.0'
+VERSION = '1.0.1'
 
 manifest {
   name = 'TRON-Bioinformatics/tronflow-vcf-normalization'
@@ -40,7 +40,7 @@ manifest {
 }
 
 params.help_message = """
-TronFlow VCF normalization v${VERSION}
+TronFlow variant normalization v${VERSION}
 
 Usage:
     nextflow run main.nf --input_files input_files --reference reference.fasta