Update RADseq_denovo workflow

RADseq_denovo/files/params.total.yml

 pipeline: RADseq_denovo
-params: {results_dir: /Results, sample_dir: /Data, sample_suffix: .fastq.gz, SeOrPe: PE,
-  quality_check: fastqc, fastqc_SE_output_dir: fastqc_SE, fastqc_PE_output_dir: fastqc_PE,
-  fastqc_threads: 4, null_output_dir: '', demultiplexing: process_radtags, process_radtags_SE_output_dir: process_radtags/SE,
-  process_radtags_barcode_file_select: server, process_radtags_barcode_file: '', process_radtags_barcode_type: --inline_null,
-  process_radtags_enzyme_SE: aciI, process_radtags_PE_output_dir: process_radtags/PE,
-  process_radtags_enzyme_1_PE: aciI, process_radtags_enzyme_2_PE: '', ustacks: ustacks,
-  ustacks_output_dir: stacks, ustacks_threads: 4, ustacks_M: 2, ustacks_m: 3, ustacks_N: NA,
-  cstacks: cstacks, cstacks_output_dir: stacks, cstacks_threads: 4, cstacks_population_tsv_select: server,
-  cstacks_population_tsv: '', cstacks_n: 1, stacks: sstacks, sstacks_output_dir: stacks,
-  sstacks_threads: 4, tsv2bam: tsv2bam, tsv2bam_output_dir: stacks, tsv2bam_threads: 4,
-  gstacks: gstacks, gstacks_output_dir: gstacks, gstacks_threads: 4, gstacks_population_tsv_select: server,
-  gstacks_population_tsv: '', gstacks_model: marukilow, gstacks_var_alpha: 0.05, gstacks_gt_alpha: 0.05,
-  gstacks_min_mapq: 20, gstacks_max_clipped: 0.2, populations: populations, populations_output_dir: populations,
-  populations_threads: 4, populations_r: 0.7, populations_max_obs_het: 1, populations_min_maf: 0.05,
-  populations_p: 2}
+params:
+  results_dir: /Results
+  sample_dir: /Data
+  sample_suffix: .fastq.gz
+  SeOrPe: PE
+  quality_check: fastqc
+  fastqc_SE_output_dir: fastqc_SE
+  fastqc_PE_output_dir: fastqc_PE
+  fastqc_threads: 4
+  null_output_dir: ''
+  demultiplexing: process_radtags
+  process_radtags_SE_output_dir: process_radtags/SE
+  process_radtags_barcode_file_select: server
+  process_radtags_barcode_file: ''
+  process_radtags_barcode_type: --inline_null
+  process_radtags_enzyme_SE: aciI
+  process_radtags_PE_output_dir: process_radtags/PE
+  process_radtags_enzyme_1_PE: aciI
+  process_radtags_enzyme_2_PE: ''
+  ustacks: ustacks
+  ustacks_output_dir: stacks
+  ustacks_threads: 4
+  ustacks_M: 2
+  ustacks_m: 3
+  ustacks_N: NA
+  cstacks: cstacks
+  cstacks_output_dir: stacks
+  cstacks_threads: 4
+  cstacks_population_tsv_select: server
+  cstacks_population_tsv: ''
+  cstacks_n: 1
+  stacks: sstacks
+  sstacks_output_dir: stacks
+  sstacks_threads: 4
+  tsv2bam: tsv2bam
+  tsv2bam_output_dir: stacks
+  tsv2bam_threads: 4
+  gstacks: gstacks
+  gstacks_output_dir: gstacks
+  gstacks_threads: 4
+  gstacks_population_tsv_select: server
+  gstacks_population_tsv: ''
+  gstacks_model: marukilow
+  gstacks_var_alpha: 0.05
+  gstacks_gt_alpha: 0.05
+  gstacks_min_mapq: 20
+  gstacks_max_clipped: 0.2
+  populations: populations
+  populations_output_dir: populations
+  populations_threads: 4
+  populations_r: 0.7
+  populations_max_obs_het: 1
+  populations_min_maf: 0.05
+  populations_p: 2
 samples: []
 groups: []
 final_step: all
 steps:
 - title: Quality check
   name: quality_check
-  tools: [fastqc, 'null']
+  tools:
+  - fastqc
+  - 'null'
   default: fastqc
 - title: Demultiplexing
   name: demultiplexing
-  tools: [process_radtags, 'null']
+  tools:
+  - process_radtags
+  - 'null'
   default: process_radtags
 - title: ustacks
   name: ustacks
-  tools: [ustacks]
+  tools:
+  - ustacks
   default: ustacks
 - title: cstacks
   name: cstacks
-  tools: [cstacks]
+  tools:
+  - cstacks
   default: cstacks
 - title: sstacks
   name: stacks
-  tools: [sstacks]
+  tools:
+  - sstacks
   default: sstacks
 - title: tsv2bam
   name: tsv2bam
-  tools: [tsv2bam]
+  tools:
+  - tsv2bam
   default: tsv2bam
 - title: gstacks
   name: gstacks
-  tools: [gstacks]
+  tools:
+  - gstacks
   default: gstacks
 - title: populations
   name: populations
-  tools: [populations]
+  tools:
+  - populations
   default: populations
 params_info:
-  results_dir: {type: output_dir}
-  sample_dir: {type: input_dir}
-  sample_suffix: {type: text}
-  SeOrPe: {type: radio}
-  fastqc_threads: {tool: fastqc, rule: fastqc_PE, type: numeric}
-  process_radtags_barcode_file_select: {tool: process_radtags, rule: process_radtags_PE,
-    type: select}
-  process_radtags_barcode_file: {tool: process_radtags, rule: process_radtags_PE,
-    type: input_file}
-  process_radtags_barcode_type: {tool: process_radtags, rule: process_radtags_PE,
-    type: select}
-  process_radtags_enzyme_SE: {tool: process_radtags, rule: process_radtags_SE, type: select}
-  process_radtags_enzyme_1_PE: {tool: process_radtags, rule: process_radtags_PE, type: select}
-  process_radtags_enzyme_2_PE: {tool: process_radtags, rule: process_radtags_PE, type: select}
-  ustacks_threads: {tool: ustacks, rule: ustacks, type: numeric}
-  ustacks_M: {tool: ustacks, rule: ustacks, type: numeric}
-  ustacks_m: {tool: ustacks, rule: ustacks, type: numeric}
-  ustacks_N: {tool: ustacks, rule: ustacks, type: numeric}
-  cstacks_threads: {tool: cstacks, rule: cstacks, type: numeric}
-  cstacks_population_tsv_select: {tool: cstacks, rule: cstacks, type: select}
-  cstacks_population_tsv: {tool: cstacks, rule: cstacks, type: input_file}
-  cstacks_n: {tool: cstacks, rule: cstacks, type: numeric}
-  sstacks_threads: {tool: sstacks, rule: sstacks, type: numeric}
-  tsv2bam_threads: {tool: tsv2bam, rule: tsv2bam, type: numeric}
-  gstacks_threads: {tool: gstacks, rule: gstacks, type: numeric}
-  gstacks_population_tsv_select: {tool: gstacks, rule: gstacks, type: select}
-  gstacks_population_tsv: {tool: gstacks, rule: gstacks, type: input_file}
-  gstacks_model: {tool: gstacks, rule: gstacks, type: select}
-  gstacks_var_alpha: {tool: gstacks, rule: gstacks, type: numeric}
-  gstacks_gt_alpha: {tool: gstacks, rule: gstacks, type: numeric}
-  gstacks_min_mapq: {tool: gstacks, rule: gstacks, type: numeric}
-  gstacks_max_clipped: {tool: gstacks, rule: gstacks, type: numeric}
-  populations_threads: {tool: populations, rule: populations, type: numeric}
-  populations_r: {tool: populations, rule: populations, type: numeric}
-  populations_max_obs_het: {tool: populations, rule: populations, type: numeric}
-  populations_min_maf: {tool: populations, rule: populations, type: numeric}
-  populations_p: {tool: populations, rule: populations, type: numeric}
-prepare_report_scripts: [populations.prepare.report.R]
+  results_dir:
+    type: output_dir
+  sample_dir:
+    type: input_dir
+  sample_suffix:
+    type: text
+  SeOrPe:
+    type: radio
+  fastqc_threads:
+    tool: fastqc
+    rule: fastqc_PE
+    type: numeric
+  process_radtags_barcode_file_select:
+    tool: process_radtags
+    rule: process_radtags_PE
+    type: select
+  process_radtags_barcode_file:
+    tool: process_radtags
+    rule: process_radtags_PE
+    type: input_file
+  process_radtags_barcode_type:
+    tool: process_radtags
+    rule: process_radtags_PE
+    type: select
+  process_radtags_enzyme_SE:
+    tool: process_radtags
+    rule: process_radtags_SE
+    type: select
+  process_radtags_enzyme_1_PE:
+    tool: process_radtags
+    rule: process_radtags_PE
+    type: select
+  process_radtags_enzyme_2_PE:
+    tool: process_radtags
+    rule: process_radtags_PE
+    type: select
+  ustacks_threads:
+    tool: ustacks
+    rule: ustacks
+    type: numeric
+  ustacks_M:
+    tool: ustacks
+    rule: ustacks
+    type: numeric
+  ustacks_m:
+    tool: ustacks
+    rule: ustacks
+    type: numeric
+  ustacks_N:
+    tool: ustacks
+    rule: ustacks
+    type: numeric
+  cstacks_threads:
+    tool: cstacks
+    rule: cstacks
+    type: numeric
+  cstacks_population_tsv_select:
+    tool: cstacks
+    rule: cstacks
+    type: select
+  cstacks_population_tsv:
+    tool: cstacks
+    rule: cstacks
+    type: input_file
+  cstacks_n:
+    tool: cstacks
+    rule: cstacks
+    type: numeric
+  sstacks_threads:
+    tool: sstacks
+    rule: sstacks
+    type: numeric
+  tsv2bam_threads:
+    tool: tsv2bam
+    rule: tsv2bam
+    type: numeric
+  gstacks_threads:
+    tool: gstacks
+    rule: gstacks
+    type: numeric
+  gstacks_population_tsv_select:
+    tool: gstacks
+    rule: gstacks
+    type: select
+  gstacks_population_tsv:
+    tool: gstacks
+    rule: gstacks
+    type: input_file
+  gstacks_model:
+    tool: gstacks
+    rule: gstacks
+    type: select
+  gstacks_var_alpha:
+    tool: gstacks
+    rule: gstacks
+    type: numeric
+  gstacks_gt_alpha:
+    tool: gstacks
+    rule: gstacks
+    type: numeric
+  gstacks_min_mapq:
+    tool: gstacks
+    rule: gstacks
+    type: numeric
+  gstacks_max_clipped:
+    tool: gstacks
+    rule: gstacks
+    type: numeric
+  populations_threads:
+    tool: populations
+    rule: populations
+    type: numeric
+  populations_r:
+    tool: populations
+    rule: populations
+    type: numeric
+  populations_max_obs_het:
+    tool: populations
+    rule: populations
+    type: numeric
+  populations_min_maf:
+    tool: populations
+    rule: populations
+    type: numeric
+  populations_p:
+    tool: populations
+    rule: populations
+    type: numeric
+prepare_report_scripts:
+- populations.prepare.report.R
 prepare_report_outputs:
-  populations: [PCA_Eigenvalues_mqc.txt, PCA_First2axis_mqc.yaml, Mean_Pairwise_Pop_FST_mqc.csv,
-    IBS_mqc.png]
+  populations:
+  - PCA_Eigenvalues_mqc.txt
+  - PCA_First2axis_mqc.yaml
+  - Mean_Pairwise_Pop_FST_mqc.csv
+  - IBS_mqc.png
 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': []
   process_radtags:
     process_radtags_SE:
-    - {name: reads_demultiplexed, file: '{individu}.fastq.gz', description: Files
-        of reads for each individual}
+    - name: reads_demultiplexed
+      file: '{individu}.fastq.gz'
+      description: Files of reads for each individual
     process_radtags_PE:
-    - {name: reads_forward_demultiplexed, file: '{individu}_R1.fastq.gz', description: Files
-        of forward reads for each individual}
-    - {name: reads_reverse_demultiplexed, file: '{individu}_R2.fastq.gz', description: Files
-        of reverse reads for each individual}
+    - name: reads_forward_demultiplexed
+      file: '{individu}_R1.fastq.gz'
+      description: Files of forward reads for each individual
+    - name: reads_reverse_demultiplexed
+      file: '{individu}_R2.fastq.gz'
+      description: Files of reverse reads for each individual
   ustacks:
     ustacks: []
   cstacks:
@@ -123,43 +282,73 @@ outputs:
     tsv2bam: []
   gstacks:
     gstacks:
-    - {name: catalog_calls, file: catalog.calls, description: Consensus sequence for
-        each assembled locus in the data}
-    - {name: catalog_fa, file: catalog.fa.gz, description: Custom file that contains
-        genotyping data}
-    - {name: stats, file: gstacks.log.distribs, description: 'Distributions statistics
-        (bam stats, coverage and phasing_rates per sample)'}
+    - name: catalog_calls
+      file: catalog.calls
+      description: Consensus sequence for each assembled locus in the data
+    - name: catalog_fa
+      file: catalog.fa.gz
+      description: Custom file that contains genotyping data
+    - name: stats
+      file: gstacks.log.distribs
+      description: Distributions statistics (bam stats, coverage and phasing_rates
+        per sample)
   populations:
     populations:
-    - {name: fstats_pop, file: 'populations.fst_{popA}-{popB}.tsv', description: SNP
-        and haplotype-based F statistics between each populations}
-    - {name: fstats_summary, file: populations.fst_summary.tsv, description: SNP and
-        haplotype-based F statistics summary}
-    - {name: haplotypes_tab, file: populations.haplotypes.tsv, description: Haplotypes
-        for each sample}
-    - {name: phistats_pop, file: 'populations.phistats_{popA}-{popB}.tsv', description: Phi
-        statistics between each populations}
-    - {name: phistats_summary, file: populations.phistats_summary.tsv, description: Phi
-        statistics summary}
-    - {name: vcf, file: populations.snps.vcf, description: SNP vcf file}
-    - {name: structure, file: populations.structure, description: Output in Structure
-        format}
-    - {name: genepop_haplotypes, file: populations.haps.genepop, description: Haplotypes
-        in GenePop format}
-    - {name: genepop_snps, file: populations.snps.genepop, description: SNP in GenePop
-        format}
-    - {name: plink_map, file: populations.plink.map, description: Genotypes in PLINK
-        format}
-    - {name: plink_ped, file: populations.plink.ped, description: Genotypes in PLINK
-        format}
-    - {name: radpainter_haplotypes, file: populations.haps.radpainter, description: Haplotypes
-        fineRADstructure/RADpainter format}
-    - {name: PCA_Eigenvalues_mqc, file: PCA_Eigenvalues_mqc.txt, description: PCA
-        eigenvalues}
-    - {name: PCA_First2axis_mqc, file: PCA_First2axis_mqc.yaml, description: PCA plot
-        on first 2 axis}
-    - {name: Mean_Pairwise_Pop_FST_mqc, file: Mean_Pairwise_Pop_FST_mqc.csv, description: Mean
-        pairwise population Fstats}
-    - {name: IBS_mqc, file: IBS_mqc.png, description: IBS heatmap}
-multiqc: {fastqc: fastqc, 'null': custom, process_radtags: custom, ustacks: custom,
-  cstacks: custom, sstacks: custom, tsv2bam: custom, gstacks: custom, populations: stacks}
+    - name: fstats_pop
+      file: populations.fst_{popA}-{popB}.tsv
+      description: SNP and haplotype-based F statistics between each populations
+    - name: fstats_summary
+      file: populations.fst_summary.tsv
+      description: SNP and haplotype-based F statistics summary
+    - name: haplotypes_tab
+      file: populations.haplotypes.tsv
+      description: Haplotypes for each sample
+    - name: phistats_pop
+      file: populations.phistats_{popA}-{popB}.tsv
+      description: Phi statistics between each populations
+    - name: phistats_summary
+      file: populations.phistats_summary.tsv
+      description: Phi statistics summary
+    - name: vcf
+      file: populations.snps.vcf
+      description: SNP vcf file
+    - name: structure
+      file: populations.structure
+      description: Output in Structure format
+    - name: genepop_haplotypes
+      file: populations.haps.genepop
+      description: Haplotypes in GenePop format
+    - name: genepop_snps
+      file: populations.snps.genepop
+      description: SNP in GenePop format
+    - name: plink_map
+      file: populations.plink.map
+      description: Genotypes in PLINK format
+    - name: plink_ped
+      file: populations.plink.ped
+      description: Genotypes in PLINK format
+    - name: radpainter_haplotypes
+      file: populations.haps.radpainter
+      description: Haplotypes fineRADstructure/RADpainter format
+    - name: PCA_Eigenvalues_mqc
+      file: PCA_Eigenvalues_mqc.txt
+      description: PCA eigenvalues
+    - name: PCA_First2axis_mqc
+      file: PCA_First2axis_mqc.yaml
+      description: PCA plot on first 2 axis
+    - name: Mean_Pairwise_Pop_FST_mqc
+      file: Mean_Pairwise_Pop_FST_mqc.csv
+      description: Mean pairwise population Fstats
+    - name: IBS_mqc
+      file: IBS_mqc.png
+      description: IBS heatmap
+multiqc:
+  fastqc: fastqc
+  'null': custom
+  process_radtags: custom
+  ustacks: custom
+  cstacks: custom
+  sstacks: custom
+  tsv2bam: custom
+  gstacks: custom
+  populations: stacks

RADseq_denovo/files/singularity.recipe → RADseq_denovo/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
 

RADseq_denovo/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