ASPICov: Automated and Standardized Pipeline for Identification of SARS-Cov2 nucleotidic Variants

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ASPICov was created to provide biologists with a fast, reliable, and comprehensive analysis of NGS SARS-Cov2 samples. This versatile application tool enables the processing of samples from either the capture or amplicon method, as well as Illumina or Ion Torrent technology. This Nextflow pipeline adheres to nf-core principles and employs Singularity containers to ensure FAIR data analysis.

Code Snippets

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"""
bamtools.sh ${bam_file}  ${sample_id}  bamtools.cmd  >& bamtools.log 2>&1
"""
NextFlow From line 17 of modules/bamtools.nf 
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"""
bcftools.sh ${vcf_file}  ${sample_id}  bcftools.cmd  >& bcftools.log 2>&1
"""
NextFlow From line 19 of modules/bcftools.nf 
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"""
bwa.sh  ${params.ref_fasta} bwa.cmd ${trimmed_files} ${sample_id} >& bwa.log 2>&1
"""
NextFlow From line 18 of modules/bwa.nf 
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"""
bwa.sh  ${params.ref_fasta} bwa2.cmd ${primerclipped_file} ${sample_id} >& bwa2.log 2>&1
"""
NextFlow From line 43 of modules/bwa.nf 
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"""
bgzip.sh ${vcf_annot_filter_pass_file}  ${sample_id}  bgzip.cmd  >& bgzip.log 2>&1
"""
NextFlow From line 16 of modules/consensus.nf 
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"""
tabix.sh ${vcf_zip_file}  ${sample_id}  tabix.cmd  >& tabix.log 2>&1
"""
NextFlow From line 37 of modules/consensus.nf 
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"""
consensus.sh ${vcf_zip_file}  ${sample_id}  ${params.ref_fasta}  consensus.cmd  >& consensus.log 2>&1
"""
NextFlow From line 57 of modules/consensus.nf 
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"""
extraction.sh  ${consensus_file_nn}  ${sample_id}  extraction.cmd  >& extraction.log 2>&1
"""
NextFlow From line 81 of modules/consensus.nf 
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"""
CoveragePlot.py ${wig_file} >& cvplot.log 2>&1
"""
NextFlow From line 15 of modules/cvplot.nf 
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"""
filter.sh  ${vcf_annot_filter_file} ${sample_id} filter.cmd  >& filter.log 2>&1
"""
NextFlow From line 19 of modules/filter.nf 
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"""
freebayes.sh ${params.ref_fasta}  ${sample_id} ${bam_ch}  freebayes.cmd  >& freebayes.log 2>&1
"""
NextFlow From line 16 of modules/freebayes.nf 
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"""
get_singularity_images.sh ${baseDir} singularity_images_ok >& get_singularity_images.log 2>&1
"""
NextFlow From line 8 of modules/get_singularity_images.nf 
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"""
get_test_data.sh ${baseDir} test_data_ok  >& get_test_data.log 2>&1
"""
NextFlow From line 14 of modules/get_test_data.nf 
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"""
igvtools.sh ${sample_id}  ${bam_ch} ${params.ref_genome}  igvtools.cmd  >& igvtools.log 2>&1
"""
NextFlow From line 17 of modules/igvtools.nf 
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"""
index.sh ${ref_fasta}  index.cmd  >& index.log 2>&1
"""
NextFlow From line 17 of modules/index.nf 
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""" 
megahit.sh ${params.technology} ${sample_id} megahit.cmd ${trimmed_files.join(' ')} >& megahit.log 2>&1
"""
NextFlow From line 20 of modules/megahit.nf 
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"""
megahit.sh ${params.technology} ${sample_id} megahit.cmd ${trimmed_files} >& megahit.log 2>&1
"""
NextFlow From line 25 of modules/megahit.nf 
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"""
normalization.sh  ${params.ref_fasta}  ${sample_id}  ${vcf_tmp_file} normalization.cmd  >& normalization.log 2>&1

"""
NextFlow From line 18 of modules/normalization.nf 
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"""
pangolin.sh "${consensus_file}"  pangolin.cmd  >& pangolin.log 2>&1
"""
NextFlow From line 19 of modules/pangolin.nf 
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"""
trimming-primers.py ${params.bedpe_file} ${samfile} ${params.ref_fasta} ${sample_id} >& primer_trimming.log 2>&1
"""
NextFlow From line 21 of modules/primer_trimming.nf 
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"""
prinseq.sh ${fastq_file}  ${sample_id}  prinseq.cmd  >& prinseq.log 2>&1
"""
NextFlow From line 16 of modules/prinseq.nf 
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"""
plots-variants.py -p . -o plot-variant.pdf >& pvariant.log 2>&1
"""
NextFlow From line 15 of modules/pvariant.nf 
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""" 
fastqc.sh ${params.technology}  ${sample_id} fastqc.cmd ${trimmed_files.join(' ')} >& fastqc.log 2>&1
"""
NextFlow From line 17 of modules/quality.nf 
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"""
fastqc.sh  ${params.technology} ${sample_id} fastqc.cmd ${trimmed_files}  >& fastqc.log 2>&1
"""
NextFlow From line 22 of modules/quality.nf 
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"""
multiqc.sh multiqc.cmd >& multiqc.log 2>&1
"""
NextFlow From line 42 of modules/quality.nf 
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"""
quast.sh ${denovo_file} ${sample_id} quast.cmd >& quast.log 2>&1
"""
NextFlow From line 22 of modules/quast.nf 
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"""
samtools.sh ${sample_id} ${sam_file} ${params.ref_fasta} ${params.ref_bed} samtools.cmd >& samtools.log 2>&1
"""
NextFlow From line 29 of modules/samtools.nf 
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"""
samtools.sh ${sample_id} ${sam2_file} ${params.ref_fasta} ${params.ref_bed} samtools2.cmd >& samtools2.log 2>&1
"""
NextFlow From line 62 of modules/samtools.nf 
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"""
snpeff.sh ${vcf_file} ${sample_id} snpeff.cmd  >& snpeff.log 2>&1
"""
NextFlow From line 19 of modules/snpeff.nf 
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"""
snpsift.sh ${vcf_annot_filter_pass_file}  ${sample_id}  snpsift.cmd  >& snpsift.log 2>&1
"""
NextFlow From line 17 of modules/snpsift.nf 
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"""
bcftools_extr.sh ${vcf_annot_filter_pass_file}  ${sample_id}  ${xls_fields_file}  bcftools_extr.cmd  >& bcftools_extr.log 2>&1
"""
NextFlow From line 40 of modules/snpsift.nf 
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"""
svh.sh . svh.cmd  >& svh.log 2>&1
"""
NextFlow From line 16 of modules/svh.nf 
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"""
synthesis1.sh . synthesis1.cmd >& synthesis1.log 2>&1
"""
NextFlow From line 16 of modules/synthesis.nf 
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"""
synthesis2.sh . synthesis2.cmd >& synthesis2.log 2>&1
"""
NextFlow From line 37 of modules/synthesis.nf 
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"""
synthesis3.sh . synthesis3.cmd >& synthesis3.log 2>&1
"""
NextFlow From line 63 of modules/synthesis.nf 
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"""
trimmomatic.sh ${task.cpus} ${reads[0]} ${reads[1]} ${sample_id} ${params.trimmomatic_adapter_file} trimmomatic.cmd >& trimmomatic.log 2>&1
"""
NextFlow From line 18 of modules/trimmomatic.nf 
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"""
vcfallelicprimitives.sh ${vcf_norm_file} ${sample_id} vcfallelicprimitives.cmd  >& vcfallelicprimitives.log 2>&1
"""
NextFlow From line 17 of modules/vcfallelicprimitives.nf
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://gitlab.com/vtilloy/aspicov
Name: aspicov
Version: Version 1
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Copyright: Public Domain
License: Apache License 2.0
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