Update Mito_Assembler_Megahit workflow

Mito_Assembler_Megahit/files/Snakefile

@@ -3,6 +3,8 @@ import re
 import snakemake.utils
 import csv
 
+dir_path = "/workflow"
+
 #############
 # Wildcards #
 #############

Mito_Assembler_Megahit/files/params.total.yml

 pipeline: Mito_Assembler_Megahit
-params: {results_dir: /Results, sample_dir: /Data, sample_suffix: .fastq.gz, SeOrPe: PE,
-  clade: Arthropoda, quality_check: fastqc, fastqc_SE_output_dir: fastqc_SE, fastqc_PE_output_dir: fastqc_PE,
-  fastqc_threads: 4, null_output_dir: '', assembling: megahit, megahit_SE_output_dir: megahit_SE,
-  megahit_threads: 4, megahit_PE_output_dir: megahit_PE, find_mitoscaf: mitoz_findmitoscaf,
-  mitoz_findmitoscaf_output_dir: mitoz_findmitoscaf, mitoz_findmitoscaf_threads: 4,
-  annotate: mitoz_annotate, mitoz_annotate_SE_output_dir: mitoz_annotate_SE, mitoz_annotate_threads: 4,
-  mitoz_annotate_PE_output_dir: mitoz_annotate_PE, visualize: igv_visualize, igv_visualize_output_dir: igv_visualize,
-  igv_visualize_threads: 4}
+params:
+  results_dir: /Results
+  sample_dir: /Data
+  sample_suffix: .fastq.gz
+  SeOrPe: PE
+  clade: Arthropoda
+  quality_check: fastqc
+  fastqc_SE_output_dir: fastqc_SE
+  fastqc_PE_output_dir: fastqc_PE
+  fastqc_threads: 4
+  null_output_dir: ''
+  assembling: megahit
+  megahit_SE_output_dir: megahit_SE
+  megahit_threads: 4
+  megahit_PE_output_dir: megahit_PE
+  find_mitoscaf: mitoz_findmitoscaf
+  mitoz_findmitoscaf_output_dir: mitoz_findmitoscaf
+  mitoz_findmitoscaf_threads: 4
+  annotate: mitoz_annotate
+  mitoz_annotate_SE_output_dir: mitoz_annotate_SE
+  mitoz_annotate_threads: 4
+  mitoz_annotate_PE_output_dir: mitoz_annotate_PE
+  visualize: igv_visualize
+  igv_visualize_output_dir: igv_visualize
+  igv_visualize_threads: 4
 samples: []
 groups: []
 final_step: all
 steps:
 - title: Quality check
   name: quality_check
-  tools: [fastqc, 'null']
+  tools:
+  - fastqc
+  - 'null'
   default: fastqc
 - title: Assembling
   name: assembling
-  tools: [megahit]
+  tools:
+  - megahit
   default: megahit
 - title: Find mitochondrion scaffold
   name: find_mitoscaf
-  tools: [mitoz_findmitoscaf]
+  tools:
+  - mitoz_findmitoscaf
   default: mitoz_findmitoscaf
 - title: Annotate
   name: annotate
-  tools: [mitoz_annotate]
+  tools:
+  - mitoz_annotate
   default: mitoz_annotate
 - title: Visualize
   name: visualize
-  tools: [igv_visualize]
+  tools:
+  - igv_visualize
   default: igv_visualize
 params_info:
-  results_dir: {type: output_dir}
-  sample_dir: {type: input_dir}
-  sample_suffix: {type: text}
-  SeOrPe: {type: radio}
-  clade: {type: radio}
-  fastqc_threads: {tool: fastqc, rule: fastqc_PE, type: numeric}
-  megahit_threads: {tool: megahit, rule: megahit_PE, type: numeric}
-  mitoz_findmitoscaf_threads: {tool: mitoz_findmitoscaf, rule: mitoz_findmitoscaf,
-    type: numeric}
-  mitoz_annotate_threads: {tool: mitoz_annotate, rule: mitoz_annotate_PE, type: numeric}
-  igv_visualize_threads: {tool: igv_visualize, rule: igv_visualize, type: numeric}
-prepare_report_scripts: [mitoz_annotate.prepare.report.R]
+  results_dir:
+    type: output_dir
+  sample_dir:
+    type: input_dir
+  sample_suffix:
+    type: text
+  SeOrPe:
+    type: radio
+  clade:
+    type: radio
+  fastqc_threads:
+    tool: fastqc
+    rule: fastqc_PE
+    type: numeric
+  megahit_threads:
+    tool: megahit
+    rule: megahit_PE
+    type: numeric
+  mitoz_findmitoscaf_threads:
+    tool: mitoz_findmitoscaf
+    rule: mitoz_findmitoscaf
+    type: numeric
+  mitoz_annotate_threads:
+    tool: mitoz_annotate
+    rule: mitoz_annotate_PE
+    type: numeric
+  igv_visualize_threads:
+    tool: igv_visualize
+    rule: igv_visualize
+    type: numeric
+prepare_report_scripts:
+- mitoz_annotate.prepare.report.R
 prepare_report_outputs:
-  mitoz_annotate: [Annotations_mqc.tsv, Contigs_mqc.tsv, Genes_found_mqc.tsv, Potential_missing_genes_mqc.tsv]
+  mitoz_annotate:
+  - Annotations_mqc.tsv
+  - Contigs_mqc.tsv
+  - Genes_found_mqc.tsv
+  - Potential_missing_genes_mqc.tsv
 outputs:
   fastqc:
     fastqc_SE:
-    - {name: html, file: '{sample}_fastqc.html', description: Rapport html fastqc}
-    - {name: zip, file: '{sample}_fastqc.zip', description: Dossier zip fastqc}
+    - name: html
+      file: '{sample}_fastqc.html'
+      description: Rapport html fastqc
+    - name: zip
+      file: '{sample}_fastqc.zip'
+      description: Dossier zip fastqc
     fastqc_PE:
-    - {name: html1, file: '{sample}_R1_fastqc.html', description: Rapport html fastqc}
-    - {name: zip1, file: '{sample}_R1_fastqc.zip', description: Dossier zip fastqc}
-    - {name: html2, file: '{sample}_R2_fastqc.html', description: Rapport html fastqc}
-    - {name: zip2, file: '{sample}_R2_fastqc.zip', description: Dossier zip fastqc}
+    - name: html1
+      file: '{sample}_R1_fastqc.html'
+      description: Rapport html fastqc
+    - name: zip1
+      file: '{sample}_R1_fastqc.zip'
+      description: Dossier zip fastqc
+    - name: html2
+      file: '{sample}_R2_fastqc.html'
+      description: Rapport html fastqc
+    - name: zip2
+      file: '{sample}_R2_fastqc.zip'
+      description: Dossier zip fastqc
   'null':
     'null': []
   megahit:
     megahit_SE:
-    - {name: contigs, file: assembly.contigs.fa, description: Result of the assembly}
+    - name: contigs
+      file: assembly.contigs.fa
+      description: Result of the assembly
     megahit_PE:
-    - {name: contigs, file: assembly.contigs.fa, description: Result of the assembly}
+    - name: contigs
+      file: assembly.contigs.fa
+      description: Result of the assembly
   mitoz_findmitoscaf:
     mitoz_findmitoscaf:
-    - {name: mitogenome, file: mitoz_findmitoscaf.mitogenome.fa, description: The
-        mitochondrial sequences from each Kmer assembly}
-    - {name: readme, file: README.txt, description: Readme with all output files explained}
+    - name: mitogenome
+      file: mitoz_findmitoscaf.mitogenome.fa
+      description: The mitochondrial sequences from each Kmer assembly
+    - name: readme
+      file: README.txt
+      description: Readme with all output files explained
   mitoz_annotate:
     mitoz_annotate_SE:
-    - {name: genbank_annots, file: mitoz_annotate_SE_mitoscaf.fa.gbf, description: The
-        mitochondrial genome in GenBank format}
-    - {name: readme, file: README.txt, description: Readme with all output files explained}
+    - name: genbank_annots
+      file: mitoz_annotate_SE_mitoscaf.fa.gbf
+      description: The mitochondrial genome in GenBank format
+    - name: readme
+      file: README.txt
+      description: Readme with all output files explained
     mitoz_annotate_PE:
-    - {name: genbank_annots, file: mitoz_annotate_PE_mitoscaf.fa.gbf, description: The
-        mitochondrial genome in GenBank format}
-    - {name: readme, file: README.txt, description: Readme with all output files explained}
+    - name: genbank_annots
+      file: mitoz_annotate_PE_mitoscaf.fa.gbf
+      description: The mitochondrial genome in GenBank format
+    - name: readme
+      file: README.txt
+      description: Readme with all output files explained
   igv_visualize:
     igv_visualize:
-    - {name: igv_png, file: '{contig_name}_mqc.png', description: Contig and read
-        coverage visualisation}
-multiqc: {fastqc: fastqc, 'null': custom, megahit: custom, mitoz_findmitoscaf: custom,
-  mitoz_annotate: custom, igv_visualize: custom}
+    - name: igv_png
+      file: '{contig_name}_mqc.png'
+      description: Contig and read coverage visualisation
+multiqc:
+  fastqc: fastqc
+  'null': custom
+  megahit: custom
+  mitoz_findmitoscaf: custom
+  mitoz_annotate: custom
+  igv_visualize: custom

Mito_Assembler_Megahit/files/singularity.recipe → Mito_Assembler_Megahit/files/singularity.def

 Bootstrap: localimage
-From: ../base.simg
+From: ../base.sif
 
 %environment
 	export PATH=/opt/biotools/bin:$PATH
@@ -17,8 +17,8 @@ From: ../base.simg
 echo "This container contains two apps (UI and Snakemake)."
 echo "UI is a user interface to set up the workflow and launch it."
 echo "Snakemake let you provide your configfile and other parameters to the snakemake command and launch it."
-echo "To get help for an app :\nsingularity help --app appName this_container.simg"
-echo "To run an app :\nsingularity run --app appName this_container.simg"
+echo "To get help for an app :\nsingularity help --app appName this_container.sif"
+echo "To run an app :\nsingularity run --app appName this_container.sif"
 
 
 ########################
@@ -30,7 +30,7 @@ echo "To run an app :\nsingularity run --app appName this_container.simg"
 %apphelp UI
 To run the UI app you should bind data and results directories like in the following example.
 You must also provide the host address and port where the shiny app will be launched
-exemple : singularity run --app UI -B /path/to/data/directory:/Data -B /path/to/store/Results:/Results this_container.simg 127.0.0.1 1234
+exemple : singularity run --app UI -B /path/to/data/directory:/Data -B /path/to/store/Results:/Results this_container.sif 127.0.0.1 1234
     
 
 ########################
@@ -46,7 +46,7 @@ exemple : singularity run --app UI -B /path/to/data/directory:/Data -B /path/to/
 %apphelp Snakemake
 To run the Snakemake app you should bind data and results directories like in the following example.
 You must also provide the configfile and the number of cores provided to snakemake command (you can add other parameters after these two)
-exemple : singularity run --app Snakemake -B /path/to/data/directory:/Data -B /path/to/store/Results:/Results this_container.simg myconfig.yml 16 otherparams
+exemple : singularity run --app Snakemake -B /path/to/data/directory:/Data -B /path/to/store/Results:/Results this_container.sif myconfig.yml 16 otherparams
     
 ########################
 # App getConfigfile
@@ -56,7 +56,7 @@ exemple : singularity run --app Snakemake -B /path/to/data/directory:/Data -B /p
 
 %apphelp getConfigfile
 To run the getConfigfile app you dont need to bind directories. This app will only copy the default parameters file from the container to your local disk.
-exemple : singularity run --app getConfigfile this_container.simg
+exemple : singularity run --app getConfigfile this_container.sif
 
 %help
 This container contains three apps (UI, Snakemake and getConfigfile).
@@ -64,9 +64,9 @@ This container contains three apps (UI, Snakemake and getConfigfile).
 * Snakemake let you provide your configfile and other parameters to the snakemake command and launch it.
 * getConfigfile give you a copy of a default parameters file to fill and use with the Snakemake app
 To get help for an app :
-singularity help --app appName this_container.simg
+singularity help --app appName this_container.sif
 To run an app :
-singularity run --app appName this_container.simg
+singularity run --app appName this_container.sif
 
 
 %files
@@ -77,6 +77,7 @@ singularity run --app appName this_container.simg
 %post
 	mkdir /Data
 	mkdir /Results
+	apt-get update -y
 
 	apt install -y fastqc=0.11.5+dfsg-6
 

Mito_Assembler_Megahit/files/tools.py

@@ -13,6 +13,6 @@ def read_yaml(filepath):
 def write_yaml(filepath,data):
     try:
         with open(filepath, 'w') as file:
-            yaml.dump(data, file)
+            yaml.dump(data, file, default_flow_style=False)
     except IOError as e:
         print("Error in file opening:", e)
\ No newline at end of file