Snakemake workflow for metagenomic analysis of rumen samples from sheep

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Code Snippets

shell:
    'cat {input.read1} {input.read2} > {output.mergedReads}'

SnakeMake From line 58 of main/Snakefile

shell:
    'fastqc '
    '-o results/fastqc/ '
    '-q ' 
    '-t {threads} '
    '{input.fastq}'

SnakeMake FastQC From line 74 of main/Snakefile

shell:
    'multiqc '
    '-n results/ReadsMultiQCReportRawData '
    '-s ' 
    '-f ' 
    '--interactive ' 
    '{input.fastqc}'

SnakeMake MultiQC From line 90 of main/Snakefile

shell:
    'kneaddata '
    '--unpaired {input.fastq} '
    '-t {threads} '
    '--log-level INFO '
    '--log {log} '
    '--trimmomatic /home/kima/conda-envs/biobakery/share/trimmomatic-0.39-2 ' 
    '--sequencer-source TruSeq3 ' # to identify correct adapter sequences
    '-db /bifo/scratch//2022-AK-MBIE-Rumen-MG/ref/ARS_UI_Ramb_v2 '
    '-db /bifo/scratch//2022-AK-MBIE-Rumen-MG/ref/SILVA_128_LSUParc_SSUParc_ribosomal_RNA '
    '-o results/kneaddata && '
    'seqkit stats -j 12 -a results/kneaddata/{wildcards.samples}*.fastq > {output.readStats}'

SnakeMake seqkit From line 123 of main/Snakefile

shell: 
    'fastqc '
    '-o results/fastqcKDR/ '
    '-q '
    '-t {threads} '
    '{input.fastqc}'

SnakeMake FastQC From line 147 of main/Snakefile

shell:
    'multiqc '
    '-n results/ReadsMultiQCReportKneadData '
    '-s '
    '-f '
    '--interactive '
    '{input.fastqc}'

SnakeMake MultiQC From line 162 of main/Snakefile

shell:
    'kraken2 '
    '--use-names '
    '--db /dataset/2022-BJP-GTDB/scratch/2022-BJP-GTDB/kraken/GTDB '
    '-t {threads} '
    '--report {output.k2ReportGTDB} '
    '--report-minimizer-data '
    '{input.KDRs} > {output.k2OutputGTDB}'

SnakeMake kraken2 From line 187 of main/Snakefile

shell: 
    'bracken '
    '-d /dataset/2022-BJP-GTDB/scratch/2022-BJP-GTDB/kraken/GTDB '
    '-i {input.k2ReportGTDB} '
    '-o {output.bOutput} '
    '-w {output.bReport} '
    '-r 240 ' # average read length
    '-l S '  # SPECIES
    '-t 10 ' # remove low abundance species (noise)  
    '&> {log} '

SnakeMake bracken From line 209 of main/Snakefile

shell: 
    'bracken '
    '-d /dataset/2022-BJP-GTDB/scratch/2022-BJP-GTDB/kraken/GTDB '
    '-i {input.k2ReportGTDB} '
    '-o {output.bOutput} '
    '-w {output.bReport} '
    '-r 240 ' # average read length
    '-l G '  # GENUS
    '-t 10 ' # remove low abundance species (noise)  
    '&> {log} '

SnakeMake bracken From line 233 of main/Snakefile

shell:
    'combine_bracken_outputs.py '
    '--files /bifo/scratch/2022-AK-MBIE-Rumen-MG/Snakemake-Metagenomics/results/brackenSpecies/*.bracken '
    '-o results/countMatrices/bracken_species.report'

SnakeMake From line 254 of main/Snakefile

shell:
    'combine_bracken_outputs.py '
    '--files /bifo/scratch/2022-AK-MBIE-Rumen-MG/Snakemake-Metagenomics/results/brackenGenus/*.bracken '
    '-o results/countMatrices/bracken_genus.report'

SnakeMake From line 268 of main/Snakefile

shell:
    'humann3 ' 
    '--memory-use minimum '
    '--threads {threads} '
    '--bypass-nucleotide-search '
    '--search-mode uniref50 '
    '--protein-database /bifo/scratch/2022-AK-MBIE-Rumen-MG/ref/humann3/unirefECFilt '
    '--input-format fastq '
    '--output results/humann3protein '
    '--input {input.KDRs} '
    '--output-basename {wildcards.samples} '
    '--o-log {log}'

SnakeMake From line 291 of main/Snakefile

shell:
    'humann_join_tables '
    '-i /bifo/scratch/2022-AK-MBIE-Rumen-MG/Snakemake-Metagenomics/results/humann3Uniref50EC '
    '--file_name genefamilies.tsv '
    '-o results/countMatrices/humann3_gene_families.tsv'

SnakeMake humann From line 312 of main/Snakefile

shell:
    'humann_join_tables '
    '-i /bifo/scratch/2022-AK-MBIE-Rumen-MG/Snakemake-Metagenomics/results/humann3Uniref50EC '
    '--file_name pathabundance.tsv '
    '-o results/countMatrices/humann3_path_abundance.tsv'

SnakeMake humann From line 326 of main/Snakefile

shell: 
    'humann_regroup_table '
    '-i {input} '
    '-c /bifo/scratch/2022-AK-MBIE-Rumen-MG/ref/humann3/utility_mapping/map_level4ec_uniref50.txt.gz '
    '-o {output}'

SnakeMake From line 340 of main/Snakefile

shell:
    'humann_rename_table '
    '-i {input} '
    '-n ec '
    '-o {output}'

SnakeMake From line 354 of main/Snakefile

shell: 
    'humann_regroup_table '
    '-i {input} '
    '-c /bifo/scratch/2022-AK-MBIE-Rumen-MG/ref/humann3/utility_mapping/map_ko_uniref50.txt.gz '
    '-o {output}'

SnakeMake From line 368 of main/Snakefile

shell:
    'humann_rename_table '
    '-i {input} '
    '-n kegg-orthology '
    '-o {output}'

SnakeMake From line 382 of main/Snakefile

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Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/alexmingikim/Snakemake-Metagenomics

Name: snakemake-metagenomics

Version: 1

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License: None

Keywords:

Sample annotation Analysis Report bracken FastQC humann kraken2 MultiQC seqkit Snakemake metagenomics

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