Snakemake pipeline for detection limit test

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detection_limit_test
detection_limit_test
detection_limit_test
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A Snakemake workflow for assessing detection limit from laser-microdissected samples.

Usage

  1. Requirements

    1. git-lfs

Code Snippets

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shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.mock} \
    2> {log} 1>&2
    """
SnakeMake Bowtie 2 From line 21 of rules/bowtie2_hosts.smk 
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shell:
    """
    if [[ {params.is_paired} = "True" ]] ; then
        (bowtie2 \
            -x {input.mock} \
            -1 {input.forward_} \
            -2 {input.reverse_} \
            --threads {threads} \
            --rg-id '{params.rg_id}' \
            --rg '{params.rg_extra}' \
            {params.extra} \
        | samtools sort \
            --threads {threads} \
            -m {params.samtools_mem} \
        | samtools rmdup - - \
        | samtools view \
            --reference {input.reference} \
            --output {output.cram} \
            --output-fmt cram,level=9,nthreads={threads} \
            --write-index \
        ) 2> {log} 1>&2
    else
        (bowtie2 \
            -x {input.mock} \
            -U {input.forward_} \
            --threads {threads} \
            --rg-id '{params.rg_id}' \
            --rg '{params.rg_extra}' \
            {params.extra} \
        | samtools sort \
            --threads {threads} \
            -m {params.samtools_mem} \
        | samtools rmdup -s - - \
        | samtools view \
            --reference {input.reference} \
            --output {output.cram} \
            --output-fmt cram,level=9,nthreads={threads} \
            --write-index \
        ) 2> {log} 1>&2
    fi
    """
SnakeMake SAMtools From line 59 of rules/bowtie2_hosts.smk 
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shell:
    """
    if [[ {params.is_paired} = "True" ]] ; then
        (samtools view \
            --reference {input.reference} \
            --threads {threads} \
            -u \
            -o /dev/stdout \
            -f 12 \
            {input.cram} \
        | samtools fastq \
            -1 {output.forward_} \
            -2 {output.reverse_} \
            -0 /dev/null \
            -c 9 \
            --threads {threads} \
        ) 2> {log} 1>&2
    else
        (samtools view \
            --reference {input.reference} \
            --threads {threads} \
            -u \
            -o /dev/stdout \
            -f 4 \
            {input.cram} \
        | samtools fastq \
            -0 {output.forward_} \
            -c 9 \
            --threads {threads} \
        ) 2> {log} 1>&2
    fi
    """
SnakeMake SAMtools From line 123 of rules/bowtie2_hosts.smk 
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shell:
    """
    bowtie2-build \
        --threads {threads} \
        {params.extra} \
        {input.reference} \
        {output.mock} \
    2> {log} 1>&2
    """
SnakeMake Bowtie 2 From line 21 of rules/bowtie2_mags.smk 
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shell:
    """
    if [[ {params.is_paired} == "True" ]] ; then
        (bowtie2 \
            -x {input.mock} \
            -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} \
            --write-index \
        ) 2> {log} 1>&2
    else
        (bowtie2 \
            -x {input.mock} \
            -U {input.forward_} \
            --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} \
            --write-index \
        ) 2> {log} 1>&2
    fi
    """
SnakeMake SAMtools From line 59 of rules/bowtie2_mags.smk 
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shell:
    """
    if [[ {params.is_paired} = True ]] ; then
        fastp \
            --in1 {input.forward_} \
            --in2 {input.reverse_} \
            --out1 >(bgzip -l 1 -@ {threads} > {output.forward_}) \
            --out2 >(bgzip -l 1 -@ {threads} > {output.reverse_}) \
            --unpaired1 >(bgzip -l 1 -@ {threads} > {output.unpaired1}) \
            --unpaired2 >(bgzip -l 1 -@ {threads} > {output.unpaired2}) \
            --html {output.html} \
            --json {output.json} \
            --compression 1 \
            --verbose \
            --adapter_sequence {params.adapter_forward} \
            --adapter_sequence_r2 {params.adapter_reverse} \
            --length_required {params.length_required} \
            --thread {threads} \
            {params.extra} \
        2> {log} 1>&2
    else
        fastp \
            --in1 {input.forward_} \
            --out1 >(bgzip -l 1 -@ {threads} > {output.forward_}) \
            --html {output.html} \
            --json {output.json} \
            --compression 1 \
            --verbose \
            --adapter_sequence {params.adapter_forward} \
            --length_required {params.length_required} \
            --thread {threads} \
            {params.extra} \
        2> {log} 1>&2
    fi
    """
SnakeMake fastp From line 26 of rules/fastp.smk 
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shell:
    "fastqc {input} 2> {log} 1>&2"
SnakeMake FastQC From line 12 of rules/fastqc.smk 
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shell:
    """
    if [[ {params.is_paired} = "True" ]] ; then
        kraken2 \
            --db {input.database} \
            --threads {threads} \
            --paired \
            --gzip-compressed \
            --output >(pigz > {output.out_gz}) \
            --report {output.report} \
            {input.forward_} \
            {input.reverse_} \
        > {log} 2>&1
    else
        kraken2 \
            --db {input.database} \
            --threads {threads} \
            --gzip-compressed \
            --output >(pigz > {output.out_gz}) \
            --report {output.report} \
            {input.forward_} \
        > {log} 2>&1
    fi
    """
SnakeMake kraken2 From line 20 of rules/kraken2.smk 
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shell:
    """
    ln --symbolic $(readlink --canonicalize {input.forward_}) {output.forward_} 2> {log}
    ln --symbolic $(readlink --canonicalize {input.reverse_}) {output.reverse_} 2> {log}
    """
SnakeMake From line 13 of rules/reads.smk 
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shell:
    """
    (gzip \
        --decompres \
        --stdout {input.fa_gz} \
    | bgzip \
        --compress-level 9 \
        --threads {threads} \
        --stdout \
        /dev/stdin \
    > {output.fa_gz} \
    ) 2> {log}
    """
SnakeMake From line 12 of rules/reference.smk 
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shell:
    """
    (gzip \
        --decompres \
        --stdout {input.fa_gz} \
    | bgzip \
        --compress-level 9 \
        --threads {threads} \
        --stdout \
        /dev/stdin \
    > {output.fa_gz} \
    ) 2> {log}
    """
SnakeMake From line 43 of rules/reference.smk 
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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 18 of rules/report_library.smk 
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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 
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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 
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shell:
    """
    multiqc \
        --title {params.title} \
        --force \
        --filename {params.title} \
        --outdir {params.dir} \
        --module kraken \
        {input} \
    2> {log} 1>&2
    """
SnakeMake MultiQC Kraken From line 61 of rules/report_step.smk 
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shell:
    """
    multiqc \
        --title {params.title} \
        --force \
        --filename {params.title} \
        --outdir {params.dir} \
        --dirs \
        --dirs-depth 1 \
        {input.reports} \
    2> {log} 1>&2
    """
SnakeMake MultiQC From line 97 of rules/report_step.smk 
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shell:
    """
    multiqc \
        --title {params.title} \
        --force \
        --filename {params.title} \
        --outdir {params.dir} \
        --dirs \
        --dirs-depth 1 \
        {input.reports} \
    2> {log} 1>&2
    """
SnakeMake MultiQC From line 135 of rules/report_step.smk 
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shell:
    "samtools flagstats {input.cram} > {output.txt} 2> {log}"
SnakeMake SAMtools From line 12 of rules/samtools.smk 
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shell:
    "samtools idxstats {input.cram} > {output.tsv} 2> {log}"
SnakeMake SAMtools From line 27 of rules/samtools.smk 
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shell:
    """
    samtools stats \
        --reference {input.reference} \
        {input.cram} \
    > {output.tsv} \
    2> {log}
    """
SnakeMake SAMtools From line 43 of rules/samtools.smk 
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shell:
    """
    samtools stats \
        --reference {input.reference} \
        {input.cram} \
    > {output.tsv} \
    2> {log}
    """
SnakeMake SAMtools From line 64 of rules/samtools.smk 
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shell:
    """
    gzip -dc {input.forward_} > {output.forward_fq} 2> {log}

    nonpareil \
        -s {output.forward_fq} \
        -T kmer \
        -b {params.prefix} \
        -f fastq \
        -t {threads} \
    2>> {log} 1>&2 || true
    """
SnakeMake nonpareil From line 28 of rules/stats.smk 
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shell:
    """
    Rscript --no-init-file workflow/scripts/aggregate_nonpareil.R \
        --input-folder {params.input_dir} \
        --output-file {output} \
    2> {log} 1>&2
    """
SnakeMake nonpareil From line 64 of rules/stats.smk 
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shell:
    """
    if [[ {params.is_paired} = "True" ]] ; then
        singlem pipe \
            --forward {input.forward_} \
            --reverse {input.reverse_} \
            --otu-table {output.otu_table} \
            --archive-otu-table {output.archive_otu_table} \
            --taxonomic-profile {output.condense} \
            --metapackage {input.data} \
            --threads {threads} \
            --assignment-threads {threads} \
        2> {log} 1>&2 || true
    else
        singlem pipe \
            --forward {input.forward_} \
            --otu-table {output.otu_table} \
            --archive-otu-table {output.archive_otu_table} \
            --taxonomic-profile {output.condense} \
            --metapackage {input.data} \
            --threads {threads} \
            --assignment-threads {threads} \
        2> {log} 1>&2 || true
    fi
    """
SnakeMake singlem From line 99 of rules/stats.smk 
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shell:
    """
    singlem condense \
        --input-archive-otu-tables {input.archive_otu_tables} \
        --taxonomic-profile {output.condense} \
        --metapackage {input.data} \
    2> {log} 1>&2
    """
SnakeMake singlem From line 151 of rules/stats.smk 
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shell:
    """
    samtools view \
        -F 4 \
        --threads {threads} \
        --reference {input.reference} \
        --output {output.bam} \
        --fast \
        {input.cram} \
    2> {log}
    """
SnakeMake SAMtools From line 190 of rules/stats.smk 
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shell:
    """
    coverm genome \
        --bam-files {input.bam} \
        --methods {params.method} \
        --separator {params.separator} \
        --min-covered-fraction {params.min_covered_fraction} \
    > {output} 2> {log} || true \
    """
SnakeMake CoverM From line 219 of rules/stats.smk 
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shell:
    """
    Rscript --no-init-file workflow/scripts/aggregate_coverm.R \
        --input-folder {params.input_dir} \
        --output-file {output} \
    2> {log} 1>&2
    """
SnakeMake From line 245 of rules/stats.smk 
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shell:
    """
    coverm contig \
        --bam-files {input.bam} \
        --methods {params.method} \
        --proper-pairs-only \
    > {output} 2> {log} || true
    """
SnakeMake CoverM From line 276 of rules/stats.smk 
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shell:
    """
    Rscript --no-init-file workflow/scripts/aggregate_coverm.R \
        --input-folder {params.input_dir} \
        --output-file {output} \
    2> {log} 1>&2
    """
SnakeMake From line 301 of rules/stats.smk
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/3d-omics/detection_limit_test
Name: detection_limit_test
Version: 1
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Copyright: Public Domain
License: MIT License
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