Workflow Steps and Code Snippets

shell:
    """
    minimap2 -ax {config[minimap2_parameter]} -t {threads} {input.assembly} {input.fastFile} \
        | samtools view -b -F 4 -@ {threads} \
        > {output.bam}
    """

shell:
    """
    minimap2 -ax {config[minimap2_parameter]} -t {threads} {input.reference} {input.fastFile} \
        | samtools view -b -F 4 -@ {threads} \
        > {output.bam}
    """

shell:
    """
    minimap2 -ax {config[minimap2_parameter]} -t {threads} {input.reference} {input.fastFile} \
        | samtools view -b -F 4 -@ {threads} \
        | samtools sort -o {output.bam}
    """

"""

minimap2 -t $task.cpus -aY --MD $genome $transcriptome > ${prefix}.align.sam

samtools sort ${prefix}.align.sam -o ${prefix}.align.sorted.bam

change_name.py  $transcriptome ${meta_t.id}.all_transcripts.fasta

"""

shell:
    """
    minimap2 -t {threads} -a {input.ref_gen} {input.contigs} > {output} 2> {log}
    """

shell:
    "minimap2 {input.flye_medaka_polypolish_pilon} {input.trimmed} -x map-ont -t {params.threads} -Y -a | samtools sort -@ 6 -l 9 -m 9G > {params.minimap_dir}/{params.prefix}_minimap_pilon_sorted.bam && samtools index {params.minimap_dir}/{params.prefix}_minimap_pilon_sorted.bam && minimap2 {input.unicycler_polypolish_pilon} {input.trimmed} -x map-ont -t {params.threads} -Y -a | samtools sort -@ 6 -l 9 -m 9G > {params.minimap_dir}/{params.prefix}_minimap_pilon_unicycler_sorted.bam && samtools index {params.minimap_dir}/{params.prefix}_minimap_pilon_unicycler_sorted.bam"

shell:
    """
    minimap2 -t {threads} -x map-ont \
    {input.ref} {input.ont_reads} \
    > {output} 2> {log}
    """

shell:
    """
    minimap2 -t {threads} -ax map-ont \
    {input.ref} {input.ont_reads} 2> {log} | \
    samtools sort -@ {threads} | \
    samtools view -b -@ {threads} -o {output}
    samtools index {output}
    """

   shell:
      """
      echo "{params.run_ID} was run using the following versions \n" > {output.version_report}
      echo "\n Name                    Version                   Build  Channel \n SAMTOOLS: \n" &>> {output.version_report}
      conda list | grep -w "^samtools" &>> {output.version_report}

      echo "\n CUTADAPT: \n" &>> {output.version_report}
      conda list | grep -w "^cutadapt" &>> {output.version_report}

      echo "\n MINIMAP2: \n" &>> {output.version_report}
      conda list | grep -w "minimap2" &>> {output.version_report}

      echo "\n PILON: \n" &>> {output.version_report}
      conda list | grep "pilon" &>> {output.version_report}

	  echo "\n QUALIMAP: \n" &>> {output.version_report}
	  conda list | grep "qualimap" &>> {output.version_report}

	  echo "\n SHOVILL: \n" &>> {output.version_report}
	  conda list | grep "shovill" &>> {output.version_report}

	  echo "\n PROKKA: \n" &>> {output.version_report}
	  conda list | grep "prokka" &>> {output.version_report}

	  echo "\n KRAKEN2: \n" &>> {output.version_report}
	  conda list | grep "kraken2" &>> {output.version_report}

	  echo "\n PYTHON: \n" &>> {output.version_report}
	  conda list | grep "^python" &>> {output.version_report}

	  echo "\n MULTIQC: \n" &>> {output.version_report}
	  conda list | grep "multiqc" &>> {output.version_report}

	  echo "\n FASTQC: \n" &>> {output.version_report}
	  conda list | grep "fastqc" &>> {output.version_report}

	  echo "\n PICARD Alignment Sumamry Metrics: \n" &>> {output.version_report}
	  conda list | grep "picard" &>> {output.version_report}

	  echo "\n {params.run_ID} was aligned against the following reference: \n {params.reference} \n Using the following genabnk file: \n {params.genbankfile} \n " &>> {output.version_report}
	  echo "\n primer sets used were: \n (1) {params.ps1} \n (2) {params.ps2}" &>> {output.version_report} > {log.versioncheck} 2>&1
      """

shell:
    """
    {mapping}
    minimap2 -ax splice:hq -uf {input.ref} {input.fa} -t {threads} | samtools view -@ 4 -Shb - | samtools sort -@ 4 -o {output.bam}
    """