Snakemake workflow: Bioinfo_Macro_Microbial_Metatranscriptomics

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Snakemake workflow: `Bioinfo_Macro_Microbial_Metatranscriptomics`

A Snakemake workflow for <description>

Usage

The usage of this workflow is described in the

Code Snippets

shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.prefix} \
    2> {log} 1>&2
    """

SnakeMake Bowtie 2 From line 17 of rules/bowtie2.smk

shell:
    """
    (bowtie2 \
        -x {params.index_prefix} \
        -1 {input.forward_} \
        -2 {input.reverse_} \
        --threads {threads} \
        --rg-id '{params.rg_id}' \
        --rg '{params.rg_extra}' \
        {params.extra} \
    | samtools sort \
        -l 9 \
        -M \
        -m {params.samtools_mem} \
        -o {output.cram} \
        --reference {input.reference} \
        --threads {threads} \
    ) 2> {log} 1>&2
    """

SnakeMake SAMtools From line 54 of rules/bowtie2.smk

shell:
    """
    samtools view \
        --threads {threads} \
        --reference {input.reference} \
        --output-fmt BAM \
        --threads {threads} \
        --output {output.bam} \
        {input.cram} \
    2> {log} 1>&2
    """

SnakeMake SAMtools From line 15 of rules/coverm.smk

shell:
    """
    coverm genome \
        --bam-files {input.bams} \
        --methods {params.methods} \
        --separator "^" \
        --threads {threads} \
        --min-covered-fraction {params.min_covered_fraction} \
    > {output} \
    2> {log}
    """

SnakeMake CoverM From line 45 of rules/coverm.smk

shell:
    """
    coverm contig \
        --bam-files {input.bams} \
        --methods {params.methods} \
        --proper-pairs-only \
    > {output} \
    2> {log}
    """

SnakeMake CoverM From line 74 of rules/coverm.smk

shell:
    """
    fastp \
        --in1 {input.forward_} \
        --in2 {input.reverse_} \
        --out1 {output.forward_} \
        --out2 {output.reverse_} \
        --unpaired1 {output.unpaired1} \
        --unpaired2 {output.unpaired2} \
        --html {output.html} \
        --json {output.json} \
        --compression 1 \
        --verbose \
        --adapter_sequence {params.adapter_forward} \
        --adapter_sequence_r2 {params.adapter_reverse} \
        --thread {threads} \
        {params.extra} \
    2> {log} 1>&2
    """

SnakeMake fastp From line 25 of rules/fastp.smk

shell:
    "fastqc {input} 2> {log} 1>&2"

SnakeMake FastQC From line 12 of rules/fastqc.smk

shell:
    """
    kraken2 \
        --db {input.database} \
        --threads {threads} \
        --paired \
        --gzip-compressed \
        --output >(pigz -11 > {output.out_gz}) \
        --report {output.report} \
        {input.forward_} \
        {input.reverse_} \
    > {log} 2>&1
    """

SnakeMake kraken2 From line 21 of rules/kraken2.smk

shell:
    """
    ln --symbolic $(readlink --canonicalize {input.forward_}) {output.forward_}
    ln --symbolic $(readlink --canonicalize {input.reverse_}) {output.reverse_}
    """

SnakeMake From line 13 of rules/reads.smk

shell:
    "gzip --decompress --stdout {input.fa} > {output.fa} 2> {log}"

SnakeMake From line 11 of rules/reference.smk

shell:
    "gzip --decompress --stdout {input.gtf} > {output.gtf}"

SnakeMake From line 25 of rules/reference.smk

shell:
    """
    (gzip -dc {input.fna} \
    | bgzip \
        -@ {threads} \
        -l 9 \
    > {output.fna}) 2> {log}
    """

SnakeMake From line 41 of rules/reference.smk

shell:
    """
    multiqc \
        --title {params.library} \
        --force \
        --filename {params.library} \
        --outdir {params.out_dir} \
        --dirs \
        --dirs-depth 1 \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC From line 25 of rules/report_library.smk

shell:
    """
    multiqc \
        --filename reads \
        --title reads \
        --force \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC From line 13 of rules/report_step.smk

shell:
    """
    multiqc \
        --title fastp \
        --force \
        --filename fastp \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC fastp From line 37 of rules/report_step.smk

shell:
    """
    multiqc \
        --title ribodetector \
        --force \
        --filename ribodetector \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC RiboDetector From line 61 of rules/report_step.smk

shell:
    """
    multiqc \
        --title kraken2 \
        --force \
        --filename kraken2 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC kraken2 From line 85 of rules/report_step.smk

shell:
    """
    multiqc \
        --title star \
        --force \
        --filename star \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC From line 109 of rules/report_step.smk

shell:
    """
    multiqc \
        --title bowtie2 \
        --force \
        --filename bowtie2 \
        --outdir {params.dir} \
        {input} \
    2> {log} 1>&2
    """

SnakeMake MultiQC Bowtie 2 From line 133 of rules/report_step.smk

shell:
    """
    ribodetector_cpu \
        --input \
            {input.forward_} \
            {input.reverse_} \
        --output \
            {output.forward_} \
            {output.reverse_} \
        --len {params.average_length} \
        --ensure rrna \
        --threads {threads} \
        --chunk_size {params.chunk_size} \
    2> {log} 1>&2
    """

SnakeMake RiboDetector From line 23 of rules/ribodetector.smk

shell:
    "samtools index {input} 2> {log} 1>&2"

SnakeMake SAMtools From line 11 of rules/samtools.smk

shell:
    "samtools index {input} 2> {log} 1>&2"

SnakeMake SAMtools From line 25 of rules/samtools.smk

shell:
    "samtools dict {input} --output {output} 2> {log} 1>&2"

SnakeMake SAMtools From line 39 of rules/samtools.smk

shell:
    "samtools dict {input} --output {output} 2> {log} 1>&2"

SnakeMake SAMtools From line 53 of rules/samtools.smk

shell:
    "tabix {input} 2> {log} 1>&2"

SnakeMake tabix From line 67 of rules/samtools.smk

shell:
    "bgzip {input} 2> {log} 1>&2"

SnakeMake From line 81 of rules/samtools.smk

shell:
    "samtools stats --reference {input.reference} {input.bam} > {output.tsv} 2> {log}"

SnakeMake SAMtools From line 97 of rules/samtools.smk

shell:
    "samtools stats --reference {input.reference} {input.cram} > {output.tsv} 2> {log}"

SnakeMake SAMtools From line 113 of rules/samtools.smk

shell:
    "samtools flagstats {input.bam} > {output.txt} 2> {log}"

SnakeMake SAMtools From line 128 of rules/samtools.smk

shell:
    "samtools flagstats {input.cram} > {output.txt} 2> {log}"

SnakeMake SAMtools From line 143 of rules/samtools.smk

shell:
    "samtools idxstats {input.bam} > {output.tsv} 2> {log}"

SnakeMake SAMtools From line 158 of rules/samtools.smk

shell:
    "samtools idxstats {input.cram} > {output.tsv} 2> {log}"

SnakeMake SAMtools From line 173 of rules/samtools.smk

shell:
    """
    STAR \
        --runMode genomeGenerate \
        --runThreadN {threads} \
        --genomeDir {output.folder} \
        --genomeFastaFiles {input.dna} \
        --sjdbGTFfile {input.gtf} \
        --sjdbOverhang {params.sjdbOverhang} \
    2> {log} 1>&2
    """

SnakeMake STAR From line 18 of rules/star.smk

shell:
    """
    ulimit -n 90000 2> {log} 1>&2

    STAR \
        --runMode alignReads \
        --runThreadN {threads} \
        --genomeDir {input.index} \
        --readFilesIn \
            {input.r1} \
            {input.r2} \
        --outFileNamePrefix {params.out_prefix} \
        --outSAMtype BAM SortedByCoordinate \
        --outSAMunmapped Within KeepPairs \
        --outReadsUnmapped Fastx \
        --readFilesCommand "gzip -cd" \
        --quantMode GeneCounts \
    2>> {log} 1>&2
    """

SnakeMake STAR From line 53 of rules/star.smk

shell:
    """
    samtools sort \
        -l 9 \
        -m 1G \
        -M \
        -o {output.cram} \
        --output-fmt CRAM \
        --reference {input.reference} \
        -@ {threads} \
        --write-index \
        {input.bam} \
    2> {log} 1>&2
    """