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Commit 46d497ac authored by mmassaviol's avatar mmassaviol
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Maj workflow MitoZ

parent 54b674f7
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MitoZ/files/Snakefile
View file @ 46d497ac
......@@ -3,8 +3,6 @@ import re
import snakemake.utils
import csv
dir_path = "/workflow"
#############
# Wildcards #
#############
......@@ -44,10 +42,10 @@ def mitoz_filter_inputs():
inputs["read2"] = expand(raw_reads()["read2"],sample=SAMPLES)
if config["trimming"] == 'cutadapt':
if (config["SeOrPe"] == "SE"):
inputs["read"] = expand(rules.cutadapt_SE.output[0],sample=SAMPLES)
inputs["read"] = expand(rules.cutadapt_SE.output.read,sample=SAMPLES)
elif (config["SeOrPe"] == "PE"):
inputs["read"] = expand(rules.cutadapt_PE.output[0],sample=SAMPLES)
inputs["read2"] = expand(rules.cutadapt_PE.output[1],sample=SAMPLES)
inputs["read"] = expand(rules.cutadapt_PE.output.read_trimmed,sample=SAMPLES)
inputs["read2"] = expand(rules.cutadapt_PE.output.read2_trimmed,sample=SAMPLES)
return inputs
def mitoz_assemble_inputs():
......@@ -62,24 +60,24 @@ def mitoz_assemble_inputs():
inputs["read2"] = expand(rules.mitoz_filter_PE.output.read2_filtered, sample=SAMPLES)
return inputs
def mitoz_findmitoscaf_inputs():
inputs = dict()
if (config["SeOrPe"] == "SE"):
inputs["fasta"] = rules.mitoz_assemble_SE.output.assemble
if (config["SeOrPe"] == "PE"):
inputs["fasta"] = rules.mitoz_assemble_PE.output.assemble
return inputs
# def mitoz_findmitoscaf_inputs():
# inputs = dict()
# if (config["SeOrPe"] == "SE"):
# inputs["fasta"] = rules.mitoz_assemble_SE.output.assemble
# if (config["SeOrPe"] == "PE"):
# inputs["fasta"] = rules.mitoz_assemble_PE.output.assemble
# return inputs
def mitoz_annotate_inputs():
inputs = dict()
if (config["SeOrPe"] == "SE"):
inputs["fastafile"] = rules.mitoz_assemble_SE.output.assemble
inputs["fastafile"] = rules.mitoz_assemble_SE.output.mitogenome
if (config["filter"] == 'null'):
inputs.update(mitoz_filter_inputs())
else:
inputs["read"] = expand(rules.mitoz_filter_SE.output.read_filtered, sample=SAMPLES)
if (config["SeOrPe"] == "PE"):
inputs["fastafile"] = rules.mitoz_findmitoscaf.output.mitogenome
inputs["fastafile"] = rules.mitoz_assemble_PE.output.mitogenome
if (config["filter"] == 'null'):
inputs.update(mitoz_filter_inputs())
else:
......@@ -87,21 +85,14 @@ def mitoz_annotate_inputs():
inputs["read2"] = expand(rules.mitoz_filter_PE.output.read2_filtered, sample=SAMPLES)
return inputs
def mitoz_visualize_inputs():
def igv_visualize_inputs():
inputs = dict()
if (config["SeOrPe"] == "SE"):
inputs["annotations"] = rules.mitoz_annotate_SE.output.annotate
if (config["filter"] == 'null'):
inputs.update(mitoz_filter_inputs())
else:
inputs["read"] = expand(rules.mitoz_filter_SE.output.read_filtered, sample=SAMPLES)
if (config["SeOrPe"] == "PE"):
inputs["annotations"] = rules.mitoz_annotate_PE.output.annotate
if (config["filter"] == 'null'):
inputs.update(mitoz_filter_inputs())
else:
inputs["read"] = expand(rules.mitoz_filter_PE.output.read_filtered, sample=SAMPLES)
inputs["read2"] = expand(rules.mitoz_filter_PE.output.read2_filtered, sample=SAMPLES)
inputs["circos_bam"] = rules.mitoz_annotate_PE.output.circos_bam
inputs["genome"] = rules.mitoz_assemble_PE.output.mitogenome
else:
inputs["circos_bam"] = rules.mitoz_annotate_SE.output.circos_bam
inputs["genome"] = rules.mitoz_assemble_SE.output.mitogenome
return inputs
......@@ -166,9 +157,9 @@ def step_outputs(step):
else:
outputs = rules.mitoz_assemble_SE.output
elif (step == "findmitoscaf"):
if(config["SeOrPe"] == "PE"):
outputs = rules.mitoz_findmitoscaf.output
#elif (step == "findmitoscaf"):
# if(config["SeOrPe"] == "PE"):
# outputs = rules.mitoz_findmitoscaf.output
elif (step == "annotate"):
if(config["SeOrPe"] == "PE"):
......@@ -176,11 +167,9 @@ def step_outputs(step):
else:
outputs = rules.mitoz_annotate_SE.output
elif (step == "visualize"):
if (step == "visualize"):
if(config["SeOrPe"] == "PE"):
outputs = rules.mitoz_visualize_PE.output
else:
outputs = rules.mitoz_visualize_SE.output
outputs = rules.igv_visualize.output
elif (step == "all"):
outputs = list(rules.multiqc.output)
......@@ -333,7 +322,8 @@ rule mitoz_assemble_SE:
input:
**mitoz_assemble_inputs()
output:
assemble = config["results_dir"]+"/mitoz_assemble_SE.result/mitoz_assemble_SE.assemble.scafSeq"
assemble = config["results_dir"]+"/mitoz_assemble_SE.result/mitoz_assemble_SE.assemble.scafSeq",
mitogenome = config["results_dir"]+"/mitoz_assemble_PE.result/work71.mitogenome.fa"
log: config["results_dir"]+'/logs/mitoz_assemble/mitoz_assemble_log.txt'
threads: config["mitoz_assemble_threads"]
params:
......@@ -355,7 +345,8 @@ rule mitoz_assemble_PE:
input:
**mitoz_assemble_inputs()
output:
assemble = config["results_dir"]+"/mitoz_assemble_PE.result/mitoz_assemble_PE.assemble.scafSeq"
assemble = config["results_dir"]+"/mitoz_assemble_PE.tmp/mitoz_assemble_PE.assembly/work71.scafSeq",
mitogenome = config["results_dir"]+"/mitoz_assemble_PE.result/work71.mitogenome.fa"
log: config["results_dir"]+'/logs/mitoz_assemble/mitoz_assemble_log.txt'
threads: config["mitoz_assemble_threads"]
params:
......@@ -378,31 +369,6 @@ rule mitoz_assemble_PE:
ruleorder: mitoz_assemble_PE > mitoz_assemble_SE
rule mitoz_findmitoscaf:
input:
**mitoz_findmitoscaf_inputs()
output:
mitogenome = config["results_dir"]+"/mitoz_findmitoscaf.result/mitoz_findmitoscaf.mitogenome.fa",
log: config["results_dir"]+'/logs/mitoz_findmitoscaf/mitoz_findmitoscaf_log.txt'
threads: config["mitoz_findmitoscaf_threads"]
params:
prefix = "mitoz_findmitoscaf",
result_dir = config["results_dir"]+"/mitoz_findmitoscaf.result",
clade = config["clade"]
shell:
# Si l'on veut eviter l'étape cal_bwa_abundance.py qui fait un mapping couteux sur tous les scaffolds de l'assemblage :
# convert Megahit to format similar to one produced by abundance estimate procedure with a dummy abundance of 0.1
"""awk '{{if (NR%2 == 1) {{split($0,a," "); split(a[4],b,"="); sub(">",">C",a[1]); print a[1]"\\t100.0\\tlength="b[2]}} else print}}' {input.fasta} > /tmp/assembly.contigs.fa; """
"/opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py findmitoscaf "
"--fastafile /tmp/assembly.contigs.fa "
"--fq_size 0 "
"--thread_number {threads} "
"--from_soaptrans "
"--outprefix {params.prefix} "
"--clade {params.clade} "
"--min_abundance 10.0 "
"|& tee {log}"
rule mitoz_annotate_SE:
input:
**mitoz_annotate_inputs()
......@@ -456,120 +422,39 @@ rule mitoz_annotate_PE:
ruleorder: mitoz_annotate_PE > mitoz_annotate_SE
# rule mitoz_visualize_SE:
# input:
# **mitoz_visualize_inputs()
# output:
# visualize = config["results_dir"]+"/mitoz_visualize_SE/mitoz_visualize_SE.circos.png"
# log: config["results_dir"]+'/logs/mitoz_visualize/mitoz_visualize_log.txt'
# threads: config["mitoz_visualize_threads"]
# params:
# prefix = "mitoz_visualize_SE",
# clade = config["clade"]
# shell:
# "/opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py visualize "
# "--fastq1 {input.read} "
# #"--fq_size 0 "
# "--gb {input.annotations} "
# "--thread_number {threads} "
# "--outprefix {params.prefix} "
# "--clade {params.clade} "
# "|& tee {log}"
# #plot IGV mapping res
# "rep={params.output_dir} "
# "cd $rep "
# "cat << EOF > igv.batch "
# "new "
# "genome {input.mitogenome} "
# "load {params.output_dir}annotate.tmp/visualize/circos.sorted.bam "
# "snapshotDirectory . "
# "expand "
# "maxPanelHeight 2500 "
# "EOF "
# "for i in `grep '>' {input.mitogenome} | sed 's/>//' | awk '{{print $1}}' ` "
# "do "
# "echo \"goto $i:1-17000\" >> igv.batch "
# "echo \"sort quality \" >> igv.batch "
# "name=$(echo $i | cut -f1 -d-) "
# "echo \"snapshot ${{name}}_mqc.png\" >> igv.batch "
# "done "
# "echo \"exit \" >> igv.batch "
# "/opt/biotools/IGV_Linux_2.6.2/igv.sh -b igv.batch ; "
# rule mitoz_visualize_PE:
# input:
# **mitoz_visualize_inputs()
# output:
# visualize = config["results_dir"]+"/mitoz_visualize_PE/mitoz_visualize_PE.circos.png"
# log: config["results_dir"]+'/logs/mitoz_visualize/mitoz_visualize_log.txt'
# threads: config["mitoz_visualize_threads"]
# params:
# output_dir = config["results_dir"]+"/mitoz_visualize_PE.result",
# prefix = "mitoz_visualize_PE",
# clade = config["clade"]
# shell:
# "/opt/biotools/release_MitoZ_v2.4-alpha/MitoZ.py visualize "
# "--fastq1 {input.read} "
# "--fastq2 {input.read2} "
# #"--fq_size 0 "
# "--gb {input.annotations} "
# "--thread_number {threads} "
# "--outprefix {params.output_dir} "
# "--clade {params.clade} "
# "|& tee {log} "
# #plot IGV mapping res
# "rep={params.output_dir} "
# "cd $rep "
# "cat << EOF > igv.batch "
# "new "
# "genome {input.mitogenome} "
# "load {params.output_dir}annotate.tmp/visualize/circos.sorted.bam "
# "snapshotDirectory . "
# "expand "
# "maxPanelHeight 2500 "
# "EOF "
# "for i in `grep '>' {input.mitogenome} | sed 's/>//' | awk '{{print $1}}' ` "
# "do "
# "echo \"goto $i:1-17000\" >> igv.batch "
# "echo \"sort quality \" >> igv.batch "
# "name=$(echo $i | cut -f1 -d-) "
# "echo \"snapshot ${{name}}_mqc.png\" >> igv.batch "
# "done "
# "echo \"exit \" >> igv.batch "
# "/opt/biotools/IGV_Linux_2.6.2/igv.sh -b igv.batch ; "
# ruleorder: mitoz_visualize_PE > mitoz_visualize_SE
rule circos_visualize:
rule igv_visualize:
input:
**circos_visualize_inputs()
**igv_visualize_inputs()
output:
circos_png = config["results_dir"]+"/"+config["circos_visualize_output_dir"]+"/circos.png"
log: config["results_dir"]+'/logs/circos_visualize/circos_visualize_log.txt'
threads: config["circos_visualize_threads"]
done = config["results_dir"]+"/"+config["igv_visualize_output_dir"]+"/igv_visualize.done"
log: config["results_dir"]+'/logs/igv_visualize/igv_visualize_log.txt'
threads: config["igv_visualize_threads"]
params:
output_dir = config["results_dir"]+"/"+config["circos_visualize_output_dir"],
output_dir = config["results_dir"]+"/"+config["igv_visualize_output_dir"],
shell:
#plot IGV mapping res
"rep={params.output_dir} "
"cd $rep "
"cat << EOF > igv.batch "
"new "
"genome {input.genome} "
"load {input.circos_bam} "
"snapshotDirectory . "
"expand "
"maxPanelHeight 2500 "
"EOF "
"for i in `grep '>' {input.genome} | sed 's/>//' | awk '{{print $1}}' ` "
"do "
"echo \"goto $i:1-17000\" >> igv.batch "
"echo \"sort quality \" >> igv.batch "
"name=$(echo $i | cut -f1 -d-) "
"echo \"snapshot ${{name}}_mqc.png\" >> igv.batch "
"done "
"echo \"exit \" >> igv.batch "
"/opt/biotools/IGV_Linux_2.6.2/igv.sh -b igv.batch ; "
"cd {params.output_dir}; "
"cat <<EOF > igv.batch\n"
"new\n"
"genome {input.genome}\n"
"load {input.circos_bam}\n"
"snapshotDirectory .\n"
"expand\n"
"maxPanelHeight 2500\n"
"EOF\n"
"for i in $(grep '>' {input.genome} | sed 's/>//' | awk '{{print $1}}')\n"
"do\n"
"echo \"goto $i:1-17000\" >> igv.batch\n"
"echo \"sort quality \" >> igv.batch\n"
"name=$(echo $i | cut -f1 -d-)\n"
"echo \"snapshot ${{name}}_mqc.png\" >> igv.batch\n"
"done\n"
"echo \"exit \" >> igv.batch\n"
#"Xvfb :10 -nolisten tcp -fp /etc/X11/fonts/misc/ &\n"
#"export DISPLAY=:10\n"
"samtools index {input.circos_bam} -@ {threads}\n"
"xvfb-run -s '-screen 0 1920x1080x24' /opt/biotools/IGV_Linux_2.6.2/igv.sh -b igv.batch ; "
"touch {output.done}"
......@@ -668,3 +553,4 @@ onerror:
shell("cat {log} > "+config["results_dir"]+"/logs/workflow_end.error")
#shell("mail -s "an error occurred" youremail@provider.com < {log}")
MitoZ/files/generate_multiqc_config.py 100755 → 100644
View file @ 46d497ac
File mode changed from 100755 to 100644
MitoZ/files/params.total.yml
View file @ 46d497ac
pipeline: MitoZ
params: {results_dir: /Results, sample_dir: /Data, sample_suffix: .fastq.gz, SeOrPe: PE,
clade: Arthropoda, trimming: 'null', cutadapt_PE_output_dir: cutadapt_PE, cutadapt_threads: 4,
cutadapt_qc_score: --quality-base=33, cutadapt_qc_min: 20, cutadapt_max_N: 0, cutadapt_a: '',
cutadapt_A: '', cutadapt_SE_output_dir: cutadapt_SE, null_output_dir: '', filter: mitoz_filter,
mitoz_filter_SE_output_dir: mitoz_filter_SE, mitoz_filter_threads: 4, mitoz_adapter_list1_select: server,
mitoz_adapter_list1: '', mitoz_Ns_number_SE: 10, mitoz_filter_PE_output_dir: mitoz_filter_PE,
mitoz_adapter_list2_PE_select: server, mitoz_adapter_list2_PE: '', mitoz_remove_duplicates_PE: true,
assemble: mitoz_assemble, mitoz_assemble_SE_output_dir: mitoz_assemble_SE, mitoz_assemble_threads: 4,
mitoz_read_length: 150, mitoz_assemble_PE_output_dir: mitoz_assemble_PE, mitoz_insert_size_PE: 250,
findmitoscaf: 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: mitoz_visualize,
mitoz_visualize_SE_output_dir: mitoz_visualize_SE, mitoz_visualize_threads: 4, mitoz_visualize_PE_output_dir: mitoz_visualize_PE}
params:
results_dir: /Results
sample_dir: /Data
sample_suffix: .fastq.gz
SeOrPe: PE
clade: Arthropoda
trimming: 'null'
cutadapt_PE_output_dir: cutadapt_PE
cutadapt_threads: 4
cutadapt_qc_score: --quality-base=33
cutadapt_qc_min: 20
cutadapt_max_N: 0
cutadapt_a: ''
cutadapt_A: ''
cutadapt_SE_output_dir: cutadapt_SE
null_output_dir: ''
filter: mitoz_filter
mitoz_filter_SE_output_dir: mitoz_filter_SE
mitoz_filter_threads: 4
mitoz_adapter_list1_select: server
mitoz_adapter_list1: ''
mitoz_Ns_number_SE: 10
mitoz_filter_PE_output_dir: mitoz_filter_PE
mitoz_adapter_list2_PE_select: server
mitoz_adapter_list2_PE: ''
mitoz_remove_duplicates_PE: true
assemble: mitoz_assemble
mitoz_assemble_SE_output_dir: mitoz_assemble_SE
mitoz_assemble_threads: 4
mitoz_read_length: 150
mitoz_assemble_PE_output_dir: mitoz_assemble_PE
mitoz_insert_size_PE: 250
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: Trimming
name: trimming
tools: [cutadapt, 'null']
tools:
- cutadapt
- 'null'
default: 'null'
- title: Filter
name: filter
tools: [mitoz_filter, 'null']
tools:
- mitoz_filter
- 'null'
default: mitoz_filter
- title: Assemble
name: assemble
tools: [mitoz_assemble]
tools:
- mitoz_assemble
default: mitoz_assemble
- title: Find Mito scaffold
name: 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: [mitoz_visualize]
default: mitoz_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}
cutadapt_threads: {tool: cutadapt, rule: cutadapt_SE, type: numeric}
cutadapt_qc_score: {tool: cutadapt, rule: cutadapt_SE, type: radio}
cutadapt_qc_min: {tool: cutadapt, rule: cutadapt_SE, type: numeric}
cutadapt_max_N: {tool: cutadapt, rule: cutadapt_PE, type: numeric}
cutadapt_a: {tool: cutadapt, rule: cutadapt_SE, type: text}
cutadapt_A: {tool: cutadapt, rule: cutadapt_PE, type: text}
mitoz_filter_threads: {tool: mitoz_filter, rule: mitoz_filter_PE, type: numeric}
mitoz_adapter_list1_select: {tool: mitoz_filter, rule: mitoz_filter_PE, type: select}
mitoz_adapter_list1: {tool: mitoz_filter, rule: mitoz_filter_PE, type: input_file}
mitoz_Ns_number_SE: {tool: mitoz_filter, rule: mitoz_filter_SE, type: numeric}
mitoz_adapter_list2_PE_select: {tool: mitoz_filter, rule: mitoz_filter_PE, type: select}
mitoz_adapter_list2_PE: {tool: mitoz_filter, rule: mitoz_filter_PE, type: input_file}
mitoz_remove_duplicates_PE: {tool: mitoz_filter, rule: mitoz_filter_PE, type: checkbox}
mitoz_assemble_threads: {tool: mitoz_assemble, rule: mitoz_assemble_PE, type: numeric}
mitoz_read_length: {tool: mitoz_assemble, rule: mitoz_assemble_PE, type: numeric}
mitoz_insert_size_PE: {tool: mitoz_assemble, rule: mitoz_assemble_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}
mitoz_visualize_threads: {tool: mitoz_visualize, rule: mitoz_visualize_PE, 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
cutadapt_threads:
tool: cutadapt
rule: cutadapt_SE
type: numeric
cutadapt_qc_score:
tool: cutadapt
rule: cutadapt_SE
type: radio
cutadapt_qc_min:
tool: cutadapt
rule: cutadapt_SE
type: numeric
cutadapt_max_N:
tool: cutadapt
rule: cutadapt_PE
type: numeric
cutadapt_a:
tool: cutadapt
rule: cutadapt_SE
type: text
cutadapt_A:
tool: cutadapt
rule: cutadapt_PE
type: text
mitoz_filter_threads:
tool: mitoz_filter
rule: mitoz_filter_PE
type: numeric
mitoz_adapter_list1_select:
tool: mitoz_filter
rule: mitoz_filter_PE
type: select
mitoz_adapter_list1:
tool: mitoz_filter
rule: mitoz_filter_PE
type: input_file
mitoz_Ns_number_SE:
tool: mitoz_filter
rule: mitoz_filter_SE
type: numeric
mitoz_adapter_list2_PE_select:
tool: mitoz_filter
rule: mitoz_filter_PE
type: select
mitoz_adapter_list2_PE:
tool: mitoz_filter
rule: mitoz_filter_PE
type: input_file
mitoz_remove_duplicates_PE:
tool: mitoz_filter
rule: mitoz_filter_PE
type: checkbox
mitoz_assemble_threads:
tool: mitoz_assemble
rule: mitoz_assemble_PE
type: numeric
mitoz_read_length:
tool: mitoz_assemble
rule: mitoz_assemble_PE
type: numeric
mitoz_insert_size_PE:
tool: mitoz_assemble
rule: mitoz_assemble_PE
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:
cutadapt:
cutadapt_PE:
- {name: read_trimmed, file: '{sample}_trimmed_R1.fq.gz', description: Reads forward
trimmed}
- {name: read2_trimmed, file: '{sample}_trimmed_R2.fq.gz', description: Reads
reverse trimmed}
- name: read_trimmed
file: '{sample}_trimmed_R1.fq.gz'
description: Reads forward trimmed
- name: read2_trimmed
file: '{sample}_trimmed_R2.fq.gz'
description: Reads reverse trimmed
cutadapt_SE:
- {name: read, file: '{sample}_trimmed.fq.gz', description: Reads trimmed}
- name: read
file: '{sample}_trimmed.fq.gz'
description: Reads trimmed
'null':
'null': []
mitoz_filter:
mitoz_filter_SE:
- {name: read_filtered, file: '{sample}.fq.gz', description: Reads filtered}
- name: read_filtered
file: '{sample}.fq.gz'
description: Reads filtered
mitoz_filter_PE:
- {name: read_filtered, file: '{sample}_R1.fq.gz', description: Reads forward
filtered}
- {name: read2_filtered, file: '{sample}_R2.fq.gz', description: Reads reverse
filtered}
- name: read_filtered
file: '{sample}_R1.fq.gz'
description: Reads forward filtered
- name: read2_filtered
file: '{sample}_R2.fq.gz'
description: Reads reverse filtered
mitoz_assemble:
mitoz_assemble_SE:
- {name: read_assembled, file: assemble.scafSeq, description: Reads assembled}
- name: read_assembled
file: assemble.scafSeq
description: Reads assembled
mitoz_assemble_PE:
- {name: read_assembled, file: assemble.scafSeq, description: Reads assembled}
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: read_assembled
file: assemble.scafSeq
description: Reads assembled
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}
mitoz_visualize:
mitoz_visualize_SE:
- {name: circos, file: circos.png, description: circos png}
mitoz_visualize_PE: []
multiqc: {cutadapt: cutadapt, 'null': custom, mitoz_filter: custom, mitoz_assemble: custom,
mitoz_findmitoscaf: custom, mitoz_annotate: custom, mitoz_visualize: custom}
- 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:
cutadapt: cutadapt
'null': custom
mitoz_filter: custom
mitoz_assemble: custom
mitoz_annotate: custom
igv_visualize: custom
MitoZ/files/singularity.recipe → MitoZ/files/singularity.def
View file @ 46d497ac
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"